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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYO-EM STRUCTURE OF THE BG505 SOSIP.664 HIV-1 ENV TRIMER WITH 3 PGV04 FABS
 
Authors :  D. Lyumkis, J. -P. Julien, I. A. Wilson, A. B. Ward
Date :  26 Oct 13  (Deposition) - 13 Nov 13  (Release) - 08 Jan 14  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  5.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Keywords :  Hiv-1 Trimeric Spike, Gp140, Sosip, Broadly Neutralizing Antibody, Pgv04, Env, Envelope Glycoprotein, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Lyumkis, J. P. Julien, N. De Val, A. Cupo, C. S. Potter, P. J. Klasse, D. R. Burton, R. W. Sanders, J. P. Moore, B. Carragher, I. A. Wilson, A. B. Ward
Cryo-Em Structure Of A Fully Glycosylated Soluble Cleaved Hiv-1 Envelope Trimer.
Science V. 342 1484 2013
PubMed-ID: 24179160  |  Reference-DOI: 10.1126/SCIENCE.1245627

(-) Compounds

Molecule 1 - BG505 SOSIP GP120
    Chains: A, E, I
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 30-504
    Gene: ENV
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - BG505 SOSIP GP41
    Chains: B, F, J
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: SEE REMARK 999
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 3 - PGV04 LIGHT CHAIN
    Chains: C, G, K
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - PGV04 HEAVY CHAIN
    Chains: D, H, L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric/Biological Unit : ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 189)

Asymmetric/Biological Unit (1, 189)
No.NameCountTypeFull Name
1UNK189Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 3J5M)

(-) SS Bonds  (39, 39)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:74
2A:119 -A:205
3A:126 -A:196
4A:131 -A:157
5A:218 -A:247
6A:228 -A:239
7A:296 -A:331
8A:378 -A:445
9A:385 -A:418
10C:23 -C:88
11C:134 -C:194
12D:22 -D:92
13D:140 -D:196
14E:54 -E:74
15E:119 -E:205
16E:126 -E:196
17E:131 -E:157
18E:218 -E:247
19E:228 -E:239
20E:296 -E:331
21E:378 -E:445
22E:385 -E:418
23G:23 -G:88
24G:134 -G:194
25H:22 -H:92
26H:140 -H:196
27I:54 -I:74
28I:119 -I:205
29I:126 -I:196
30I:131 -I:157
31I:218 -I:247
32I:228 -I:239
33I:296 -I:331
34I:378 -I:445
35I:385 -I:418
36K:23 -K:88
37K:134 -K:194
38L:22 -L:92
39L:140 -L:196

(-) Cis Peptide Bonds  (27, 27)

Asymmetric/Biological Unit
No.Residues
1Glu A:49 -Thr A:50
2Pro A:124 -Leu A:125
3Thr A:135 -Asn A:136
4Thr A:139 -Asp A:140
5Ala A:436 -Pro A:437
6Ser C:7 -Pro C:8
7Tyr C:140 -Pro C:141
8Phe D:146 -Pro D:147
9Glu D:148 -Pro D:149
10Glu E:49 -Thr E:50
11Pro E:124 -Leu E:125
12Thr E:135 -Asn E:136
13Thr E:139 -Asp E:140
14Ala E:436 -Pro E:437
15Ser G:7 -Pro G:8
16Tyr G:140 -Pro G:141
17Phe H:146 -Pro H:147
18Glu H:148 -Pro H:149
19Glu I:49 -Thr I:50
20Pro I:124 -Leu I:125
21Thr I:135 -Asn I:136
22Thr I:139 -Asp I:140
23Ala I:436 -Pro I:437
24Ser K:7 -Pro K:8
25Tyr K:140 -Pro K:141
26Phe L:146 -Pro L:147
27Glu L:148 -Pro L:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J5M)

(-) Exons   (0, 0)

(no "Exon" information available for 3J5M)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:415
 aligned with Q2N0S6_9HIV1 | Q2N0S6 from UniProtKB/TrEMBL  Length:860

    Alignment length:447
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       
        Q2N0S6_9HIV1     43 VWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCTVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIE  489
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee.......hhhhhhhhh..ee......eee.....ee.hhhhhhhhhhhhhhhhhhhhhh..............ee...............eeeeee..........eeeeee..--------------------.........ee......................eeeee.........ee..eeee.............eee.........eee..........eeeeeeeeeeeeee.........eeee..eee............eeeeehhhhhhhhhhhhhhhhhhhh.....eee......hhhhhheeeee..eeeee.hhhhh.eee..------------...eeeee.ee..eee....eee..........eeeeeeeeeeeee.........eeeee....hhhhhhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j5m A   44 VWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYR--------------------YRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWIS------------NDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    53        63        73        83        93       103       113       123       133       143 ||    161       171      |  -         -       193       203       213       223       233       243       253       263       273       283       293       303     ||314       324       334       344       354       364       374       384       394  |      -     | 415       425       435       445       455       465       475       485       
                                                                                                                               145|                     178                  191                                                                                                                   309|                                                                                   397          411                                                                                 
                                                                                                                                154                                                                                                                                                                 311                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:63
                                                                                                
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                3j5m B    9 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  134
                            ||||||||18||||||||28|||||||101|||||||111|||||||121|||||||131|||
                            9-UNK|||18-UNK|||27-UNK|||36-UNK||108-UNK||117-UNK||126-UNK||||
                            10-UNK|||19-UNK|||28-UNK|||37-UNK||109-UNK||118-UNK||127-UNK|||
                             11-UNK|| 20-UNK|| 29-UNK||101-UNK||110-UNK||119-UNK||128-UNK||
                              12-UNK|  21-UNK|  30-UNK| 102-UNK| 111-UNK| 120-UNK| 129-UNK|
                               13-UNK   22-UNK   31-UNK  103-UNK  112-UNK  121-UNK  130-UNK
                                14-UNK   23-UNK   32-UNK  104-UNK  113-UNK  122-UNK  131-UNK
                                 15-UNK   24-UNK   33-UNK  105-UNK  114-UNK  123-UNK  132-UNK
                                  16-UNK   25-UNK   34-UNK  106-UNK  115-UNK  124-UNK  133-UNK
                                   17-UNK   26-UNK   35-UNK  107-UNK  116-UNK  125-UNK  134-UNK


Chain C from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhhhh..eeeeee.......eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j5m C    1 EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20      ||32        42        52        62        72        82        96       106       116       126       136       146       156       166       176       186       196       206        
                                                     27|                                                           91|                                                                                                                      
                                                      30                                                            96                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eee.....eeeeee.hhhhhhheeeeeeeee......eeeeeee.....eee.hhhhhhheeeeee....eeeeee...hhhhheeeeeeeee................eeeee........eeee.........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j5m D    1 QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30     |  39        49   ||   57        67        77     |||84        94      100D||     108       118       128||     140       150       160       170       180       190       200       210     
                                                             35A               52A|                            82A||               100A|||||                          129|                                                                                   
                                                                                52B                             82B|                100B||||                           132                                                                                   
                                                                                                                 82C                 100C|||                                                                                                                 
                                                                                                                                      100D||                                                                                                                 
                                                                                                                                       100E|                                                                                                                 
                                                                                                                                        100F                                                                                                                 


Chain E from PDB  Type:PROTEIN  Length:415
 aligned with Q2N0S6_9HIV1 | Q2N0S6 from UniProtKB/TrEMBL  Length:860

    Alignment length:447
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       
        Q2N0S6_9HIV1     43 VWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCTVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIE  489
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee.......hhhhhhhhh..ee......eee.....ee.hhhhhhhhhhhhhhhhhhhhhh..............ee...............eeeeee..........eeeeee..--------------------.........ee......................eeeee.........ee..eeee.............eee.........eee..........eeeeeeeeeeeeee.........eeee..eee............eeeeehhhhhhhhhhhhhhhhhhhh.....eee......hhhhhheeeee..eeeee.hhhhh.eee..------------...eeeee.ee..eee....eee..........eeeeeeeeeeeee.........eeeee....hhhhhhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j5m E   44 VWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYR--------------------YRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWIS------------NDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    53        63        73        83        93       103       113       123       133       143 ||    161       171      |  -         -       193       203       213       223       233       243       253       263       273       283       293       303     ||314       324       334       344       354       364       374       384       394  |      -     | 415       425       435       445       455       465       475       485       
                                                                                                                               145|                     178                  191                                                                                                                   309|                                                                                   397          411                                                                                 
                                                                                                                                154                                                                                                                                                                 311                                                                                                                                                                                    


Chain F from PDB  Type:PROTEIN  Length:63
                                                                                                
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                3j5m F    9 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  134
                            ||||||||18||||||||28|||||||101|||||||111|||||||121|||||||131|||
                            9-UNK|||18-UNK|||27-UNK|||36-UNK||108-UNK||117-UNK||126-UNK||||
                            10-UNK|||19-UNK|||28-UNK|||37-UNK||109-UNK||118-UNK||127-UNK|||
                             11-UNK|| 20-UNK|| 29-UNK||101-UNK||110-UNK||119-UNK||128-UNK||
                              12-UNK|  21-UNK|  30-UNK| 102-UNK| 111-UNK| 120-UNK| 129-UNK|
                               13-UNK   22-UNK   31-UNK  103-UNK  112-UNK  121-UNK  130-UNK
                                14-UNK   23-UNK   32-UNK  104-UNK  113-UNK  122-UNK  131-UNK
                                 15-UNK   24-UNK   33-UNK  105-UNK  114-UNK  123-UNK  132-UNK
                                  16-UNK   25-UNK   34-UNK  106-UNK  115-UNK  124-UNK  133-UNK
                                   17-UNK   26-UNK   35-UNK  107-UNK  116-UNK  125-UNK  134-UNK


Chain G from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhhhh..eeeeee.......eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j5m G    1 EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20      ||32        42        52        62        72        82        96       106       116       126       136       146       156       166       176       186       196       206        
                                                     27|                                                           91|                                                                                                                      
                                                      30                                                            96                                                                                                                      


Chain H from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eee.....eeeeee.hhhhhhheeeeeeeee......eeeeeee.....eee.hhhhhhheeeeee....eeeeee...hhhhheeeeeeeee................eeeee........eeee.........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j5m H    1 QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30     |  39        49   ||   57        67        77     |||84        94      100D||     108       118       128||     140       150       160       170       180       190       200       210     
                                                             35A               52A|                            82A||               100A|||||                          129|                                                                                   
                                                                                52B                             82B|                100B||||                           132                                                                                   
                                                                                                                 82C                 100C|||                                                                                                                 
                                                                                                                                      100D||                                                                                                                 
                                                                                                                                       100E|                                                                                                                 
                                                                                                                                        100F                                                                                                                 


Chain I from PDB  Type:PROTEIN  Length:415
 aligned with Q2N0S6_9HIV1 | Q2N0S6 from UniProtKB/TrEMBL  Length:860

    Alignment length:447
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       
        Q2N0S6_9HIV1     43 VWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCTVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIE  489
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee.......hhhhhhhhh..ee......eee.....ee.hhhhhhhhhhhhhhhhhhhhhh..............ee...............eeeeee..........eeeeee..--------------------.........ee......................eeeee.........ee..eeee.............eee.........eee..........eeeeeeeeeeeeee.........eeee..eee............eeeeehhhhhhhhhhhhhhhhhhhh.....eee......hhhhhheeeee..eeeee.hhhhh.eee..------------...eeeee.ee..eee....eee..........eeeeeeeeeeeee.........eeeee....hhhhhhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j5m I   44 VWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYR--------------------YRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWIS------------NDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    53        63        73        83        93       103       113       123       133       143 ||    161       171      |  -         -       193       203       213       223       233       243       253       263       273       283       293       303     ||314       324       334       344       354       364       374       384       394  |      -     | 415       425       435       445       455       465       475       485       
                                                                                                                               145|                     178                  191                                                                                                                   309|                                                                                   397          411                                                                                 
                                                                                                                                154                                                                                                                                                                 311                                                                                                                                                                                    


Chain J from PDB  Type:PROTEIN  Length:63
                                                                                                
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                3j5m J    9 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  134
                            ||||||||18||||||||28|||||||101|||||||111|||||||121|||||||131|||
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                                   17-UNK   26-UNK   35-UNK  107-UNK  116-UNK  125-UNK  134-UNK


Chain K from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhhhh..eeeeee.......eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j5m K    1 EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20      ||32        42        52        62        72        82        96       106       116       126       136       146       156       166       176       186       196       206        
                                                     27|                                                           91|                                                                                                                      
                                                      30                                                            96                                                                                                                      


Chain L from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eee.....eeeeee.hhhhhhheeeeeeeee......eeeeeee.....eee.hhhhhhheeeeee....eeeeee...hhhhheeeeeeeee................eeeee........eeee.........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j5m L    1 QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30     |  39        49   ||   57        67        77     |||84        94      100D||     108       118       128||     140       150       160       170       180       190       200       210     
                                                             35A               52A|                            82A||               100A|||||                          129|                                                                                   
                                                                                52B                             82B|                100B||||                           132                                                                                   
                                                                                                                 82C                 100C|||                                                                                                                 
                                                                                                                                      100D||                                                                                                                 
                                                                                                                                       100E|                                                                                                                 
                                                                                                                                        100F
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3J5M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J5M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J5M)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,E,I   (Q2N0S6_9HIV1 | Q2N0S6)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q2N0S6_9HIV1 | Q2N0S6: 5v7j 5v8l 5v8m 5viy 5vj6 5w6d
UniProtKB/TrEMBL
        Q2N0S6_9HIV1 | Q2N0S6: 4nco 4zmj 5aco 5c7k 5cez 5cjx 5d9q 5fyl 5i8h 5js9 5jsa 5t3s 5t3x 5t3z 5thr 5u1f 5utf 5uty

(-) Related Entries Specified in the PDB File

4nco