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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC-PG20 IN COMPLEX WITH HIV-1 CLADE A/E 93TH057 GP120
 
Authors :  T. Zhou, S. Moquin, P. D. Kwong
Date :  23 Jul 13  (Deposition) - 21 Aug 13  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Neutralizing Antibody Vrc-Pg20, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Zhou, J. Zhu, X. Wu, S. Moquin, B. Zhang, P. Acharya, I. S. Georgiev, H. R. Altae-Tran, G. Y. Chuang, M. G. Joyce, Y. Do Kwon, N. S. Longo, M. K. Louder, T. Luongo, K. Mckee, C. A. Schramm, J. Skinner, Y. Yang, Z. Yang, Z. Zhang, A. Zheng, M. Bonsignori, B. F. Haynes, J. F. Scheid, M. C. Nussenzweig, M. Simek, D. R. Burton, W. C. Koff, J. C. Mullikin, M. Connors, L. Shapiro, G. J. Nabel, J. R. Mascola, P. D. Kwong
Multidonor Analysis Reveals Structural Elements, Genetic Determinants, And Maturation Pathway For Hiv-1 Neutralization By Vrc01-Class Antibodies.
Immunity V. 39 245 2013
PubMed-ID: 23911655  |  Reference-DOI: 10.1016/J.IMMUNI.2013.04.012

(-) Compounds

Molecule 1 - HIV-1 CLADE A/E STRAIN 93TH057 GP120
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: 93TH057
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY VRC-PG20
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - LIGHT CHAIN OF ANTIBODY VRC-PG20
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    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  (5, 18)

Asymmetric/Biological Unit (5, 18)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU G:52 , ALA G:73 , GLN G:103 , ASP G:107 , TYR G:217 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:634BINDING SITE FOR RESIDUE EPE G 511
02AC2SOFTWARELYS G:282 , THR G:283 , THR G:455 , GLY G:472 , GLY G:473 , HOH G:687 , TRP H:50 , GLN H:56BINDING SITE FOR RESIDUE EDO G 512
03AC3SOFTWARESER G:256 , LEU G:453 , GLY G:472 , GLY G:473 , ASN G:474 , ILE G:475 , ASN G:478 , HOH G:617BINDING SITE FOR RESIDUE EDO G 513
04AC4SOFTWAREPCA H:1 , VAL H:2 , HIS H:102BINDING SITE FOR RESIDUE EDO H 301
05AC5SOFTWAREGLN H:101 , HIS H:102 , TRP H:103 , HOH H:418 , HOH L:441BINDING SITE FOR RESIDUE EDO H 302
06AC6SOFTWAREARG H:75 , LYS H:210 , HOH H:466BINDING SITE FOR RESIDUE CL H 303
07AC7SOFTWAREGLN H:39 , GLY H:42 , GLN L:38 , TYR L:39 , ALA L:40 , ASP L:41 , TYR L:85 , HOH L:407 , HOH L:420BINDING SITE FOR RESIDUE EDO L 301
08AC8SOFTWAREASN G:234 , THR G:236 , HIS G:352 , HOH G:633BINDING SITE FOR MONO-SACCHARIDE NAG G 501 BOUND TO ASN G 234
09AC9SOFTWAREASN G:229 , LYS G:231 , ASN G:241BINDING SITE FOR MONO-SACCHARIDE NAG G 502 BOUND TO ASN G 241
10BC1SOFTWAREASP G:211 , PRO G:212 , LYS G:252 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , HOH G:609 , HOH G:611BINDING SITE FOR MONO-SACCHARIDE NAG G 503 BOUND TO ASN G 262
11BC2SOFTWAREASN G:276 , THR G:278 , ARG H:100A , SER L:27 , THR L:31BINDING SITE FOR MONO-SACCHARIDE NAG G 504 BOUND TO ASN G 276
12BC3SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLN G:344BINDING SITE FOR MONO-SACCHARIDE NAG G 505 BOUND TO ASN G 289
13BC4SOFTWAREASN G:295 , GLU G:332BINDING SITE FOR MONO-SACCHARIDE NAG G 506 BOUND TO ASN G 295
14BC5SOFTWAREASN G:334 , THR G:336 , LYS G:337 , HOH G:627BINDING SITE FOR MONO-SACCHARIDE NAG G 507 BOUND TO ASN G 334
15BC6SOFTWAREASN G:354 , ASN G:355 , PRO L:109BINDING SITE FOR MONO-SACCHARIDE NAG G 508 BOUND TO ASN G 355
16BC7SOFTWAREGLN G:117 , GLN G:203 , ASN G:386 , THR G:388BINDING SITE FOR MONO-SACCHARIDE NAG G 509 BOUND TO ASN G 386
17BC8SOFTWARESER G:291 , ASN G:448 , HOH G:641BINDING SITE FOR MONO-SACCHARIDE NAG G 510 BOUND TO ASN G 448

(-) SS Bonds  (13, 13)

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
11H:216 -L:211
12L:23 -L:88
13L:134 -L:193

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr G:463 -Ser G:464
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LSU)

(-) 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:346
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhhhee.......ee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee......eeeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhhhhhhhh..........eeeeeeee.eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lsu G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  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      |406       416       426       436       446       456       466       476       486      
                                                                                                          124|                                                                                                   300|                            355|                                     397|                                                                                        
                                                                                                           198                                                                                                    324                             357                                      404                                                                                        


Chain H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee............ee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4lsu H    1 xVHLMQSGTEMKKPGASVRVTCQTSGYTFSDYFIHWLRQVPGRGFEWMGWMNPQWGQVNYARTFQGRVTMTRDVYREVAYLDLRSLTFADTAVYFCARRMRSQDREWDFQHWGQGTRIIVSSASTKGPSVFPLAPSSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                            |       10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121      |134       144       154       164       174       184       194       204       214  
                            1-PCA                                             52A                            82A||               100A||||                         128|                                                                                    
                                                                                                              82B|                100B|||                          132                                                                                    
                                                                                                               82C                 100C||                                                                                                                 
                                                                                                                                    100D|                                                                                                                 
                                                                                                                                     100E                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                            
               SCOP domains d4lsul1 L:2-107 automated matches                                                                  d4lsul2 L:108-211 automated matches                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeee.......eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee..ee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhh....eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lsu L    2 SALTQPPSVSGSPGQSITLSCTGASTSVAWYQQYADKAPRLIVFDGNKRPSDISSRFSGSQSGGTASLTISGLQSEDEAYYHCNAFEFFGGGTKLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTEC  211
                                   |12        22    ||  35        45        55        65        75        85     || 99       108       118       128       138       148       158       168       178       188       198       208   
                                   9|              27|                                                          91|       106A                                                                                                         
                                   11               31                                                           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 4LSU)

(-) Pfam Domains  (0, 0)

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

(-) 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 ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Thr G:463 - Ser G:464   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  4lsu
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  Q0ED31_9HIV1 | Q0ED31
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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 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 4j6r 4jb9 4jpv 4jpw