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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT
 
Authors :  N. I. Nicely, S. M. Dennison, G. Kelsoe, H. -X. Liao, S. M. Alam, B. F. Hayn
Date :  22 Apr 10  (Deposition) - 17 Nov 10  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hiv-1, Hiv, Gp41, Mper, 13H11, 2F5, Z13, 4E10, Fab Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. I. Nicely, S. M. Dennison, L. Spicer, R. M. Scearce, G. Kelsoe, Y. Ueda, H. Chen, H. X. Liao, S. M. Alam, B. F. Haynes
Crystal Structure Of A Non-Neutralizing Antibody To The Hiv-1 Gp41 Membrane-Proximal External Region.
Nat. Struct. Mol. Biol. V. 17 1492 2010
PubMed-ID: 21076400  |  Reference-DOI: 10.1038/NSMB.1944

(-) Compounds

Molecule 1 - ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T CELL
    Expression System Common: HUMAN
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: FUSION PROTEIN BETWEEN MOUSE FV AND A HUMAN FC
    Organism Common: MOUSE,HUMAN
    Organism Scientific: MUS MUSCULUS,HOMO SAPIENS
    Organism Taxid: 10090,9606
 
Molecule 2 - ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T CELL
    Expression System Common: HUMAN
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: FUSION PROTEIN BETWEEN MOUSE FV AND A HUMAN FC
    Organism Common: MOUSE,HUMAN
    Organism Scientific: MUS MUSCULUS,HOMO SAPIENS
    Organism Taxid: 10090,9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3NO31Ligand/IonNITRATE ION
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3NO3-1Ligand/IonNITRATE ION
4SO44Ligand/IonSULFATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NO31Ligand/IonNITRATE ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER B:21 , LYS B:23 , HOH B:318 , HOH B:325BINDING SITE FOR RESIDUE SO4 B 231
02AC2SOFTWAREARG B:66 , LYS B:83 , HOH B:251BINDING SITE FOR RESIDUE SO4 B 232
03AC3SOFTWARELEU B:0 , SER B:25 , GLY B:26 , HOH B:286 , ASN C:30A , ARG C:30C , TYR C:32BINDING SITE FOR RESIDUE SO4 B 233
04AC4SOFTWARELYS A:39 , GLN A:42 , HOH A:255 , GLY D:26BINDING SITE FOR RESIDUE SO4 A 217
05AC5SOFTWARELYS C:39 , GLN C:42 , LYS C:45 , HOH C:255BINDING SITE FOR RESIDUE SO4 C 217
06AC6SOFTWAREASN B:216 , PRO C:59 , ASP C:60 , HOH C:332BINDING SITE FOR RESIDUE SO4 C 218
07AC7SOFTWARETRP A:96 , THR A:97 , PHE A:98 , HOH A:275 , LEU B:45 , LYS B:46 , TRP B:47 , HOH B:310 , HOH B:393BINDING SITE FOR RESIDUE EDO B 234
08AC8SOFTWARETHR A:178 , HOH A:225 , HOH A:242 , LEU B:143 , VAL B:177 , SER B:186 , LEU B:187 , SER B:188 , HOH B:252BINDING SITE FOR RESIDUE EDO B 235
09AC9SOFTWAREALA C:12 , GLU C:105 , ILE C:106 , TYR C:140 , GLN C:166 , TYR C:173 , HOH C:304BINDING SITE FOR RESIDUE EDO C 219
10BC1SOFTWAREILE B:2 , LEU B:4 , HIS B:102 , TRP B:103 , ASP D:31 , TYR D:32BINDING SITE FOR RESIDUE EDO B 236
11BC2SOFTWARESER B:33 , ASN B:52BINDING SITE FOR RESIDUE CL B 237
12BC3SOFTWARESER C:28BINDING SITE FOR RESIDUE NO3 C 220

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:142 -B:208
5C:23 -C:88
6C:134 -C:194
7D:22 -D:92
8D:142 -D:208

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Thr A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:148 -Pro B:149
5Glu B:150 -Pro B:151
6Ser C:7 -Pro C:8
7Thr C:94 -Pro C:95
8Tyr C:140 -Pro C:141
9Phe D:148 -Pro D:149
10Glu D:150 -Pro D:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MNV)

(-) Sequences/Alignments

Asymmetric 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:221
 aligned with Q8TCD0_HUMAN | Q8TCD0 from UniProtKB/TrEMBL  Length:239

    Alignment length:238
                                                                               53                                                                                                                                                                                         
                                                                             52 |                                                                                                                                                                                         
                                    11        21        31        41        51| |     60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q8TCD0_HUMAN     2 RLPAQLLGLLMLWVPGSSGDVVMTQSPLSLPVTLGQPASISCRSTQSLVYS-DGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKITRVEAEDVGVYFCMQGTHWPSTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 238
               SCOP domains d3                 mnva1 A:-1-107 automated matches                                                                                 d3mnva2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnv A  -1 RL-----------------DIQLTQSPSSLAMSGGQKVTMRCKSSQSLLNSRNERNYLAWYQQKPGQSPKLLVYFASIRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCLQHYNTPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                             |       -         1        11        21       30A|||||   35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                             0                 1                           30A|||||                                                                                                                                                                                       
                                                                            30B||||                                                                                                                                                                                       
                                                                             30C|||                                                                                                                                                                                       
                                                                              30D||                                                                                                                                                                                       
                                                                               30E|                                                                                                                                                                                       
                                                                                30F                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with Q6N089_HUMAN | Q6N089 from UniProtKB/TrEMBL  Length:472

    Alignment length:225
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238     
         Q6N089_HUMAN    19 CEVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGSIAYADSVKGRFTISRDNGKNSLYLQMNSLRAEDTALYYCAKEIGAHNFYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 243
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee..----------.ee...eeeee........eeeee..-------.eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnv B   0 LQIQLVQSGPELKKPGETVKISCKASGYTFTDYSVHWVKQVPGKGLKWMGWINTETGEPTYADDFKGRFAFSLESSASTAYLEIHNLKNEDTATYFCALGW----------LHWGLGTTLTVSSASTKGPSVFPLAP-------GTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 226
                                     9        19        29        39        49   |    58        68        78    ||| 85        95|        - |     109       119      |  -    |  141       151  |||| 166  ||   177  ||   188       198 |||   211       221     
                                                                               52A                            82A||            96        101                      126     136               154|||    169|      180|               200||                     
                                                                                                               82B|                                                                          156||     171       182                203|                     
                                                                                                                82C                                                                           157|                                   205                     
                                                                                                                                                                                               162                                                           


Chain C from PDB  Type:PROTEIN  Length:220
 aligned with Q8TCD0_HUMAN | Q8TCD0 from UniProtKB/TrEMBL  Length:239

    Alignment length:237
                                                                               53                                                                                                                                                                                        
                                                                             52 |                                                                                                                                                                                        
                                    11        21        31        41        51| |     60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         Q8TCD0_HUMAN     2 RLPAQLLGLLMLWVPGSSGDVVMTQSPLSLPVTLGQPASISCRSTQSLVYS-DGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKITRVEAEDVGVYFCMQGTHWPSTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 237
               SCOP domains d3                 mnvc1 C:-1-107 automated matches                                                                                 d3mnvc2 C:108-212 automated matches                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnv C  -1 RL-----------------DIQLTQSPSSLAMSGGQKVTMRCKSSQSLLNSRNERNYLAWYQQKPGQSPKLLVYFASIRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCLQHYNTPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                             |       -         1        11        21       30A|||||   35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                             0                 1                           30A|||||                                                                                                                                                                                      
                                                                            30B||||                                                                                                                                                                                      
                                                                             30C|||                                                                                                                                                                                      
                                                                              30D||                                                                                                                                                                                      
                                                                               30E|                                                                                                                                                                                      
                                                                                30F                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:208
 aligned with Q6N089_HUMAN | Q6N089 from UniProtKB/TrEMBL  Length:472

    Alignment length:224
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    
         Q6N089_HUMAN    20 EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGSIAYADSVKGRFTISRDNGKNSLYLQMNSLRAEDTALYYCAKEIGAHNFYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 243
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeee...----------......eeeee........eeeee...------.eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnv D   1 QIQLVQSGPELKKPGETVKISCKASGYTFTDYSVHWVKQVPGKGLKWMGWINTETGEPTYADDFKGRFAFSLESSASTAYLEIHNLKNEDTATYFCALGW----------LHWGLGTTLTVSSASTKGPSVFPLAPS------GTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 226
                                    10        20        30        40        50  |     59        69        79   |||  86        96         -|      110       120      |  -   |   142       152 ||||  167 ||    178 ||    189       199|||    212       222    
                                                                              52A                            82A||            96        101                       127    136               154|||    169|      180|               200||                     
                                                                                                              82B|                                                                          156||     171       182                203|                     
                                                                                                               82C                                                                           157|                                   205                     
                                                                                                                                                                                              162
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  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  (1, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3MNV)

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  3mnv
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  Q6N089_HUMAN | Q6N089
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  Q8TCD0_HUMAN | Q8TCD0
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q6N089_HUMAN | Q6N089: 2oqj 3qct 3qcu 3qcv 4nm4 4nm8 4nuj 5ewi 5ug0
        Q8TCD0_HUMAN | Q8TCD0: 1hzh 1n0x 3mnw 3mnz 3pgf 4d9q 4nug 4nuj 4nwt 5viy 5vj6 5vod
UniProtKB/TrEMBL
        Q6N089_HUMAN | Q6N089: 1u6a 3cfj 3cfk 4hpy
        Q8TCD0_HUMAN | Q8TCD0: 3cfj 3cfk 4nwu

(-) Related Entries Specified in the PDB File

3mnw CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT WITH A GP41 MPER-DERIVED PEPTIDE IN A HELICAL CONFORMATION
3mnz CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT WITH A GP41 MPER-DERIVED PEPTIDE BEARING ALA SUBSTITUTIONS IN A HELICAL CONFORMATION
3mo1 CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT
3moa CRYSTAL STRUCTURE OF THE NEUTRALIZING HIV ANTIBODY 2F5 FAB FRAGMENT (RECOMBINANTLY PRODUCED FAB) WITH 17 AA GP41 MPER- DERIVED PEPTIDE
3mob CRYSTAL STRUCTURE OF THE NEUTRALIZING HIV ANTIBODY 2F5 FAB FRAGMENT (RECOMBINANTLY PRODUCED FAB) WITH 11 AA GP41 MPER- DERIVED PEPTIDE
3mod CRYSTAL STRUCTURE OF THE NEUTRALIZING HIV ANTIBODY 2F5 FAB FRAGMENT (RECOMBINANTLY PRODUCED IGG) WITH 11 AA GP41 MPER- DERIVED PEPTIDE