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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTIBODY VRC07-G54R IN COMPLEX WITH CLADE A/E 93TH057 HIV-1 GP120 CORE
 
Authors :  Y. D. Kwon, P. D. Kwong
Date :  25 Jan 14  (Deposition) - 03 Sep 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Vrc07 Antibody, Passive Transfer, Neutralization, In Vivo Protection, Autoreactivity, Lentiviral Infection, Enhanced Potency, Hiv-1 Gp120, Vrc07-G54R, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Rudicell, Y. D. Kwon, S. Y. Ko, A. Pegu, M. K. Louder, I. S. Georgiev X. Wu, J. Zhu, J. C. Boyington, X. Chen, W. Shi, Z. Y. Yang, N. A. Doria-Rose, K. Mckee, S. O'Dell, S. D. Schmidt, G. Y. Chuang, A. Druz, C. Soto, Y. Yang, B. Zhang, T. Zhou, J. P. Todd, K. E. Lloyd, J. Eudailey, K. E. Roberts, B. R. Donald, R. T. Bailer, J. Ledgerwood, J. C. Mullikin, L. Shapiro, R. A. Koup, B. S. Graham, M. C. Nason, M. Connors, B. F. Haynes, S. S. Rao, M. Roederer, P. D. Kwong, J. R. Mascola, G. J. Nabel
Enhanced Potency Of A Broadly Neutralizing Hiv-1 Antibody I Vitro Improves Protection Against Lentiviral Infection In Vivo.
J. Virol. V. 88 12669 2014
PubMed-ID: 25142607  |  Reference-DOI: 10.1128/JVI.02213-14

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PVRC8400
    Expression System Strain: 293F CELLS
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 43-122, 201-303, 325-486
    Gene: ENV, POL
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: HIV-1 GP120 WITH LEADER SEQUENCE
    Strain: 93TH057
 
Molecule 2
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PVRC8400
    Expression System Strain: 293F CELLS
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CODON-OPTIMIZED HUMAN ANTIBODY HEAVY CHAIN OF VRC01
 
Molecule 3
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PVRC8400
    Expression System Strain: 293F CELLS
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: LIGHT CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CODON-OPTIMIZED HUMAN ANTIBODY LIGHT CHAIN OF VRC01

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : GHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN G:234 , HIS G:352 , GLN H:192BINDING SITE FOR RESIDUE NAG G 501
02AC2SOFTWAREASP G:230 , LYS G:231 , ASN G:232 , ASN G:241BINDING SITE FOR RESIDUE NAG G 502
03AC3SOFTWAREASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , NAG G:510 , HOH G:603 , HOH G:625 , HOH G:650BINDING SITE FOR RESIDUE NAG G 503
04AC4SOFTWAREGLU G:275 , ASN G:276 , HOH G:624 , SER L:30 , TYR L:91BINDING SITE FOR RESIDUE NAG G 504
05AC5SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , LYS G:348 , HOH G:608BINDING SITE FOR RESIDUE NAG G 505
06AC6SOFTWAREASN G:295 , THR G:297 , TYR G:330 , GLU G:332 , HOH G:633BINDING SITE FOR RESIDUE NAG G 506
07AC7SOFTWAREASN G:334 , LYS G:337 , THR G:413BINDING SITE FOR RESIDUE NAG G 507
08AC8SOFTWAREGLN G:117 , ASN G:386 , THR G:388BINDING SITE FOR RESIDUE NAG G 508
09AC9SOFTWAREASN G:392 , CYS G:410BINDING SITE FOR RESIDUE NAG G 509
10BC1SOFTWARESER G:291 , ASN G:448 , NAG G:503BINDING SITE FOR RESIDUE NAG G 510

(-) SS Bonds  (14, 14)

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:32 -H:98
11H:140 -H:196
12H:216 -L:216
13L:23 -L:88
14L:136 -L:196

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Ser L:7 -Pro L:8
4Tyr L:142 -Pro L:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OLY)

(-) 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:342
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhheee.......eee....eeee.hhhhhhhhhhhhhhhhhhh.....eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee......eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.................eeeeeeeee.eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4oly G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 329       339       349     ||360       370       380       390      |410       420       430       440       450       460       470       480       490  
                                                                                                          124|                                                                                                    301|                           355|                                     397|                                                                                    
                                                                                                           198                                                                                                     325                            357                                      408                                                                                    


Chain H from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee............eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4oly H    1 QVRLSQSGGQMKKPGDSMRISCRASGYEFINCPINWIRLAPGKRPEWMGWMKPRGGAVSYARQLQGRVTMTRDMYSETAFLELRSLTSDDTAVYFCTRGKYCTARDYYNWDFEHWGQGTPVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128       138       148       158       168       178       188       198       208        
                                                                              52A                            82A||               100A|||||||                                                                                                                    
                                                                                                              82B|                100B||||||                                                                                                                    
                                                                                                               82C                 100C|||||                                                                                                                    
                                                                                                                                    100D||||                                                                                                                    
                                                                                                                                     100E|||                                                                                                                    
                                                                                                                                      100F||                                                                                                                    
                                                                                                                                       100G|                                                                                                                    
                                                                                                                                        100H                                                                                                                    


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.....eeeeeee.....eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeee.........eeeee....hhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4oly L    3 VLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYTLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  216
                                    12        22       |34        44        54        64        74        84      ||98       108       118       128       138       148       158       168       178       188       198       208        
                                                      30|                                                        91|                                                                                                                        
                                                       33                                                         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  (0, 0)

(no "SCOP Domain" information available for 4OLY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
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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 4jpw 4lsp 4lsq 4lsr 4lsu 4olu 4olv 4olw 4olx 4olz 4om0 4om1 4p9h 4rfn 4rfo 4rz8 4xnz 4xvt 4ydj 4ydk 4ydl 4yfl

(-) Related Entries Specified in the PDB File

4olu 4olv 4olw 4olx 4olz 4om0 4om1