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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY 12A21 IN COMPLEX WITH HIV-1 STRAIN 93TH057 GP120 MUTANT
 
Authors :  P. Acharya, T. Luongo, T. Zhou, P. D. Kwong
Date :  19 Mar 13  (Deposition) - 17 Apr 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Hiv, Gp120, Cd4-Binding Site, 12A21, Neutralization, Vaccine, Antibody, Envelope Protein, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Klein, R. Diskin, J. F. Scheid, C. Gaebler, H. Mouquet, I. S. Georgiev, M. Pancera, T. Zhou, R. B. Incesu, B. Z. Fu, P. N. Gnanapragasam, T. Y. Oliveira, M. S. Seaman, P. D. Kwong, P. J. Bjorkman, M. C. Nussenzweig
Somatic Mutations Of The Immunoglobulin Framework Are Generally Required For Broad And Potent Hiv-1 Neutralization.
Cell(Cambridge, Mass. ) V. 153 126 2013
PubMed-ID: 23540694  |  Reference-DOI: 10.1016/J.CELL.2013.03.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY 12A21
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - LIGHT CHAIN OF ANTIBODY 12A21
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : GHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN G:234 , ILE G:272 , SER G:274 , HIS G:352BINDING SITE FOR RESIDUE NAG G 501
02AC2SOFTWAREGLU G:83 , ASN G:229 , ASN G:241BINDING SITE FOR RESIDUE NAG G 502
03AC3SOFTWAREASP G:211 , LYS G:252 , VAL G:254 , ASN G:262 , ASN G:377 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , NAG G:510 , HOH G:613BINDING SITE FOR RESIDUE NAG G 503
04AC4SOFTWAREASN G:276 , THR G:278 , GLY L:28 , ILE L:29 , SER L:32BINDING SITE FOR RESIDUE NAG G 504
05AC5SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289BINDING SITE FOR RESIDUE NAG G 505
06AC6SOFTWAREASN G:295 , GLU G:332BINDING SITE FOR RESIDUE NAG G 506
07AC7SOFTWAREPRO G:81 , GLU G:83 , ASN G:334 , THR G:336 , LYS G:337BINDING SITE FOR RESIDUE NAG G 507
08AC8SOFTWAREGLN G:203 , ASN G:386 , THR G:388BINDING SITE FOR RESIDUE NAG G 508
09AC9SOFTWAREASN G:392 , CYS G:395 , MET G:407 , LYS G:408 , CYS G:410BINDING SITE FOR RESIDUE NAG G 509
10BC1SOFTWARESER G:291 , ASN G:448 , NAG G:503 , HOH G:628BINDING SITE FOR RESIDUE NAG G 510
11BC2SOFTWARELEU G:52 , HIS G:72 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:615BINDING SITE FOR RESIDUE EPE G 511

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1G:54 -G:74
2G:119 -G:205
3G:218 -G:247
4G:228 -G:239
5G:296 -G:331
6G:378 -G:445
7G:385 -G:418
8G:395 -G:410
9H:22 -H:92
10H:140 -H:196
11L:23 -L:88
12L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1His H:101 -Pro H:102
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Ser L:7 -Pro L:8
5Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JPW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JPW)

(-) Exons   (0, 0)

(no "Exon" information available for 4JPW)

(-) 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 G from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhhhee......eeee....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.......eeeeeeehhhhhhhhhhhhhhhhh.....eeee......hhhhhheeeee..eeeee.hhhhhhhhhhh.......eeeeeeee..eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jpw G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIGTMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348      |359       369       379       389       407       417       427       437       447       457       467       477       487     
                                                                                                          124|                                                                                                    301|                            355|                                     397|                                                                                      
                                                                                                           198                                                                                                     324                             357                                      406                                                                                      


Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee....eeeeeeee...hhhhh.eeeeee......eeeeeee....eeee.......eeeeee....eeeeeee..hhhhheeeeeeee.hhhhh...eeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jpw H    2 QHLVQSGTQVKKPGASVRVSCQASGYTFTNYILHWWRQAPGQGLEWMGLIKPVFGAVNYARQFQGRIQLTRDIYREIAFLDLSGLRSDDTAVYYCARDESGDDLKWHLHPWGQGTQVIVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    11        21       |32   |    41        51 |||    60        70        80  |||   87        97  |||||102       112       122       132       142       152       162       172       182       192       202       212   
                                                      29|  35A               52A||                          82A||              100A|||||                                                                                                                   
                                                       31                     52B|                           82B|               100B||||                                                                                                                   
                                                                                54                            82C                100C|||                                                                                                                   
                                                                                                                                  100D||                                                                                                                   
                                                                                                                                   100E|                                                                                                                   
                                                                                                                                    100F                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains d4jpwl1 L:1-107 automated matches                                                                      d4jpwl2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jpw L    1 DIQMTQSPSSLSASVGDRVTINCQAGQGIGSSLNWYQKKPGRAPKLLVHGASNLQRGVPSRFSGSGFHTTFTLTISSLQPDDVATYFCAVFQWFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90||     104       114       124       134       144       154       164       174       184       194       204        
                                                                                                                     91|                                                                                                                    
                                                                                                                      96
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JPW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JPW)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        Q0ED31_9HIV1 | Q0ED31: 3ngb 3se8 3se9 3tgt 3u7y 4dko 4dkp 4dkq 4dkr 4dku 4dkv 4dvs 4dvt 4dvv 4dvw 4dvx 4h8w 4i54 4jb9 4jdt 4jkp 4jpv 4lsp 4lsq 4lsr 4lsu 4olu 4olv 4olw 4olx 4oly 4olz 4om0 4om1 4p9h 4rfn 4rfo 4rz8 4xnz 4xvt 4ydj 4ydk 4ydl 4yfl

(-) Related Entries Specified in the PDB File

3ngb 3se8 3se9 4gw4 4jpv