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(-) Description

Title :  STRUCTURE OF SIMIAN IMMUNODEFICIENCY VIRUS ENVELOPE SPIKES BOUND WITH CD4 AND MONOCLONAL ANTIBODY 36D5
 
Authors :  G. Hu, J. Liu, K. Roux, K. A. Taylor
Date :  25 Nov 15  (Deposition) - 10 May 17  (Release) - 10 May 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  NOT APPLICABLE
Chains :  Asym./Biol. Unit :  A,B,C,D,E,I
Keywords :  Cryoelectron Tomography, Immunology, Aids, Hiv, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Hu, J. Liu, K. H. Roux, K. A. Taylor
Structure Of Simian Immunodeficiency Virus Envelope Spikes Bound With Cd4 And Monoclonal Antibody 36D5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP120
    Chains: A, E, I
    Fragment: SEE REMARK 999
    Organism Common: SIV
    Organism Scientific: SIMIAN IMMUNODEFICIENCY VIRUS
    Organism Taxid: 11723
    Strain: SIV239/251TAIL/SUPT-CCR5 CL.30
 
Molecule 2 - ANTIBODY 36D5 LIGHT CHAIN
    Chains: B
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ANTIBODY 36D5 HEAVY CHAIN
    Chains: C
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - T-CELL SURFACE GLYCOPROTEIN CD4
    Chains: D
    Fragment: UNP RESIDUES 26-200
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: T-CELL SURFACE ANTIGEN T4/LEU-3

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3JCC)

(-) Sites  (0, 0)

(no "Site" information available for 3JCC)

(-) SS Bonds  (33, 33)

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
10B:23 -B:88
11B:135 -B:194
12C:22 -C:92
13C:138 -C:194
14D:16 -D:84
15D:130 -D:159
16E:54 -E:74
17E:119 -E:205
18E:126 -E:196
19E:131 -E:157
20E:218 -E:247
21E:228 -E:239
22E:296 -E:331
23E:378 -E:445
24E:385 -E:418
25I:54 -I:74
26I:119 -I:205
27I:126 -I:196
28I:131 -I:157
29I:218 -I:247
30I:228 -I:239
31I:296 -I:331
32I:378 -I:445
33I:385 -I:418

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Thr A:123 -Pro A:124
2Tyr B:141 -Pro B:142
3Lys B:167 -Tyr B:173
4Phe C:144 -Pro C:145
5Glu C:146 -Pro C:147
6Thr E:123 -Pro E:124
7Thr I:123 -Pro I:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JCC)

(-) 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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eee........hhhhhhhhhhee.......................hhhhhhhhhhhhhhhhhh.............eee..............eeeeeeee......eeeeeeee............ee.............eee....eeeeee.............eeee.............eee.........eeee.........eeeeeeeeeeeeeee.......ee.......ee...........eeeee.hhhhhhhhhhhhhhhhhhh....eeee......hhhhhheeee....eeee........ee.........eeeeeeee.ee........ee........eeeeeeeeeeeeeee.......eeeeee...hhhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3jcc A   44 VWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEP  493
                                    53        63        73        83        93       103       113       123       133      |151       161       171      |193       203       213       223       233       243       253       263       273       283       293       303     ||314       324       334       344       354       364       374       384       394      |413       423       433       443       453       463       473       483       493
                                                                                                                          140|                          178|                                                                                                                   309|                                                                                       401|                                                                                  
                                                                                                                           149                           191                                                                                                                    311                                                                                        411                                                                                  


Chain B from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee.......eeeeeeee......eeee.............eee.........eeeee...hhhhh.eeeeeeee............eeeee........eeeee..hhhhhh...eeeeeeee.......eeeeee..ee....eee.......eeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3jcc B    8 TFVSVAPGQTARITCGEESLGSRSVIWYQQRPGQAPSLIIYNNNDRPSGIPDRFSGSPGSTFGTTATLTITSVEAGDEADYYCHIWDSRRPTNWVFGEGTTLIVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAP  209
                             ||     18        28        38        48        58       67A||      75        85        95|||    102       112       122       132       142       152       162    || 177       187       197       207  
                             9|                                                      67A||                          95A||                                                                     167|                                    
                             11                                                       67B|                           95B|                                                                      173                                    
                                                                                       67C                            95C                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee......eeeeee......ee.......eeeeee....eeeeee...hhhhheeeeeeeeeeeee..hhhhhhhheeeeeeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee......eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3jcc C    1 QVHLQESGPGLVKPSETLSLTCNVSGTLVRDNYWSWIRQPLGKQPEWIGYVHDSGDTNYNPSLKSRVHLSLDKSKNLVSLRLTGVTAADSAIYYCATTKHGRRIYGVVAFKEWFTYFYMDVWGKGTSVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSGTQTYICNVNHKPSNTKVDKRVEP  211
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G||||||100Q|      109       119      |133       143       153       163       173       183 ||    195       205      
                                                                                                            82A||               100A|||||100J||||||||                       126|                                                   185|                       
                                                                                                             82B|                100B|||||100K|||||||                        131                                                    188                       
                                                                                                              82C                 100C|||||100L||||||                                                                                                         
                                                                                                                                   100D|||||100M|||||                                                                                                         
                                                                                                                                    100E|||| 100N||||                                                                                                         
                                                                                                                                     100F|||  100O|||                                                                                                         
                                                                                                                                      100G||   100P||                                                                                                         
                                                                                                                                       100H|    100Q|                                                                                                         
                                                                                                                                        100I     100R                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeee.........eeee....eeeeee..eeee........ee.hhhhhhh.eeeeee...hhhhheeeeeee..eeeeeeeeeeeeee...........eeeeee.......eeeee.....eeee..eeee...hhhhheeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3jcc D    1 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIV  175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain E from PDB  Type:PROTEIN  Length:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eee........hhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhh............ee...............eeeeeeee......eeeeeeee............ee.............eee.....eeeee.............eeee.............eee.........eeee.........eeee....eeeeeee......eee.......eee..........eeeeehhhhhhhhhhhhhhhhhhhh....eeee......hhhhhheeee....eeee.hhhhh..ee.........eeeeeeee.ee........ee........eeeeeeeeeeeeeee.......eeeeee...hhhhhhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3jcc E   44 VWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEP  493
                                    53        63        73        83        93       103       113       123       133      |151       161       171      |193       203       213       223       233       243       253       263       273       283       293       303     ||314       324       334       344       354       364       374       384       394      |413       423       433       443       453       463       473       483       493
                                                                                                                          140|                          178|                                                                                                                   309|                                                                                       401|                                                                                  
                                                                                                                           149                           191                                                                                                                    311                                                                                        411                                                                                  


Chain I from PDB  Type:PROTEIN  Length:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eee........hhhhhhhhhhh........................hhhhhhhhhhhhhhhhhh.............ee...............eeeeeeee......eeeeeeee............ee.............eee.....eeeee.............eeee.............eee.........eeee.........eeeeeeeeeeeeeee.......eee.....eee...........eeeeehhhhhhhhhhhhhhhhhhhh....eeee......hhhhhheeee....eeee........ee.........eeeeeeee.eee......eee........eeeeeeeeeeeeeee.......eeeeee...hhhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3jcc I   44 VWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEP  493
                                    53        63        73        83        93       103       113       123       133      |151       161       171      |193       203       213       223       233       243       253       263       273       283       293       303     ||314       324       334       344       354       364       374       384       394      |413       423       433       443       453       463       473       483       493
                                                                                                                          140|                          178|                                                                                                                   309|                                                                                       401|                                                                                  
                                                                                                                           149                           191                                                                                                                    311                                                                                        411
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 3JCC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (55, 55)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu C:146 - Pro C:147   [ RasMol ]  
    Lys B:167 - Tyr B:173   [ RasMol ]  
    Phe C:144 - Pro C:145   [ RasMol ]  
    Thr A:123 - Pro A:124   [ RasMol ]  
    Thr E:123 - Pro E:124   [ RasMol ]  
    Thr I:123 - Pro I:124   [ RasMol ]  
    Tyr B:141 - Pro B:142   [ RasMol ]  
 

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  3jcc
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  CD4_HUMAN | P01730
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 Related Entries

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

UniProtKB/Swiss-Prot
        CD4_HUMAN | P01730: 1cdh 1cdi 1cdj 1cdu 1cdy 1g9m 1g9n 1gc1 1jl4 1opn 1opt 1opw 1q68 1rzj 1rzk 1wbr 1wio 1wip 1wiq 2b4c 2jkr 2jkt 2klu 2nxy 2nxz 2ny0 2ny1 2ny2 2ny3 2ny4 2ny5 2ny6 2qad 3b71 3cd4 3j70 3jcb 3jwd 3jwo 3lqa 3o2d 3s4s 3s5l 3t0e 4h8w 4jm2 4p9h 4q6i 4r2g 4r4h 4rqs 5a7x 5a8h 5cay 5thr 5u1f 5vn3

(-) Related Entries Specified in the PDB File

3jcb