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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC-PG04 IN COMPLEX WITH HIV-1 GP120
 
Authors :  P. D. Kwong, T. Zhou
Date :  10 Jun 11  (Deposition) - 10 Aug 11  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Hiv, Gp120, Antibody, Vrc-Pg04, Neutralization, Vaccine, Envelope Glycoprotein, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Wu, T. Zhou, J. Zhu, B. Zhang, I. Georgiev, C. Wang, X. Chen, N. S. Longo, M. Louder, K. Mckee, S. O'Dell, S. Perfetto, S. D. Schmidt, W. Shi, L. Wu, Y. Yang, Z. Y. Yang, Z. Yang, Z. Zhang, M. Bonsignori, J. A. Crump, S. H. Kapiga, N. E. Sam, B. F. Haynes, M. Simek, D. R. Burton, W. C. Koff, N. A. Doria-Rose, M. Connors, J. C. Mullikin, G. J. Nabel, M. Roederer, L. Shapiro, P. D. Kwong, J. R. Mascola
Focused Evolution Of Hiv-1 Neutralizing Antibodies Revealed By Structures And Deep Sequencing.
Science V. 333 1593 2011
PubMed-ID: 21835983  |  Reference-DOI: 10.1126/SCIENCE.1207532

(-) Compounds

Molecule 1 - HIV-1 CLADE AE STRAIN 93TH057 GP120
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PVRC8400
    Expression System Strain: 293F
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: CORE GP120 WITH TRANCATIONS
    Gene: GP120
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: 93TH057
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY VRC-PG04
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: CMVR DERIVED PLASMIDS FOR IGG1
    Expression System Strain: 293F CELLS
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: ANTIGEN BINDING FRAGEMENT OF HEAVY CHAIN
    Gene: ANTIBODY VRC-PG04 HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - LIGHT CHAIN OF ANTIBODY VRC-PG04
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: CMVR DERIVED PLASMIDS FOR IGG1
    Expression System Strain: 293F CELLS
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: ANTIBODY LIGHT CHAIN
    Gene: ANTIBODY VRC-PG04 LIGHT CHAIN
    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  (6, 39)

Asymmetric/Biological Unit (6, 39)
No.NameCountTypeFull Name
1BU31Ligand/Ion(R,R)-2,3-BUTANEDIOL
2CL18Ligand/IonCHLORIDE ION
3GOL4Ligand/IonGLYCEROL
4NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO45Ligand/IonSULFATE ION
6TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN G:234 , THR G:236 , HIS G:352 , HOH G:507 , CL G:1015BINDING SITE FOR RESIDUE NAG G 734
02AC2SOFTWAREASN G:229 , LYS G:231 , ASN G:241BINDING SITE FOR RESIDUE NAG G 741
03AC3SOFTWAREHOH G:6 , LYS G:252 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , HOH G:508 , HOH G:596 , HOH G:650BINDING SITE FOR RESIDUE NAG G 762
04AC4SOFTWAREASN G:276 , HOH G:503 , GOL G:1007 , GLY H:100A , GLY H:100C , GLY L:31 , HIS L:32 , LEU L:91BINDING SITE FOR RESIDUE NAG G 776
05AC5SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , LYS G:348 , HOH G:577 , HOH G:637 , SO4 G:1002BINDING SITE FOR RESIDUE NAG G 789
06AC6SOFTWAREASN G:295 , GLU G:332 , LYS G:442 , HOH G:589 , HOH G:680BINDING SITE FOR RESIDUE NAG G 795
07AC7SOFTWAREPRO G:79 , PRO G:81 , ASN G:334 , LYS G:337BINDING SITE FOR RESIDUE NAG G 834
08AC8SOFTWAREMET G:373 , ASN G:386 , THR G:388 , HOH G:585BINDING SITE FOR RESIDUE NAG G 886
09AC9SOFTWAREGLN G:389 , ASN G:392 , CYS G:395 , MET G:407 , GLY G:409 , CYS G:410BINDING SITE FOR RESIDUE NAG G 892
10BC1SOFTWARESER G:291 , ASN G:448 , HOH G:512 , HOH G:543 , HOH G:661BINDING SITE FOR RESIDUE NAG G 948
11BC2SOFTWAREHOH G:24 , HOH G:171 , ASN G:474 , LYS G:476 , ARG G:480 , HOH G:633 , HOH G:667 , TYR H:98BINDING SITE FOR RESIDUE SO4 G 1000
12BC3SOFTWAREARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:536 , GOL G:1005BINDING SITE FOR RESIDUE SO4 G 1001
13BC4SOFTWARELYS G:290 , LYS G:340 , GLN G:344 , NAG G:789BINDING SITE FOR RESIDUE SO4 G 1002
14BC5SOFTWAREASP G:107 , ILE G:423 , HOH G:623 , SO4 G:1001BINDING SITE FOR RESIDUE GOL G 1005
15BC6SOFTWAREASP G:230 , LYS G:231 , PHE G:233 , GLU G:267 , ILE G:271 , ARG G:273 , TYR G:484 , LYS G:485 , HOH G:500BINDING SITE FOR RESIDUE GOL G 1006
16BC7SOFTWAREASN G:276 , LEU G:277 , THR G:278 , HOH G:503 , NAG G:776 , CL G:1015BINDING SITE FOR RESIDUE GOL G 1007
17BC8SOFTWAREGLY G:124 , GLY G:429 , THR G:430 , GLY G:431 , ARG H:73 , ASP H:74BINDING SITE FOR RESIDUE GOL G 1008
18BC9SOFTWAREHOH G:8 , HOH G:32 , PRO G:363 , ASN G:386 , THR G:388 , HOH G:585BINDING SITE FOR RESIDUE CL G 1013
19CC1SOFTWAREALA G:58 , HOH G:547 , HOH G:605BINDING SITE FOR RESIDUE CL G 1014
20CC2SOFTWARELEU G:277 , NAG G:734 , GOL G:1007BINDING SITE FOR RESIDUE CL G 1015
21CC3SOFTWAREILE G:109 , ASP G:113 , GLN G:428BINDING SITE FOR RESIDUE CL G 1016
22CC4SOFTWAREHIS G:249 , GLY G:250BINDING SITE FOR RESIDUE CL G 1017
23CC5SOFTWARETRP G:69 , HIS G:72 , GLN G:114BINDING SITE FOR RESIDUE CL G 1019
24CC6SOFTWAREPRO G:299 , SER G:300BINDING SITE FOR RESIDUE CL G 1022
25CC7SOFTWAREILE G:272 , LYS G:348 , HIS G:352 , HOH G:540BINDING SITE FOR RESIDUE CL G 1027
26CC8SOFTWAREMET G:434BINDING SITE FOR RESIDUE CL G 1028
27CC9SOFTWAREHOH G:163 , ASP G:368 , GLU G:370 , ASN G:425 , MET G:426 , VAL H:52B , THR H:53BINDING SITE FOR RESIDUE BU3 G 1030
28DC1SOFTWAREPRO H:61 , ASP H:62 , HOH H:356BINDING SITE FOR RESIDUE CL H 1010
29DC2SOFTWARESER H:127 , LYS H:129 , ALA H:137 , PHE L:116BINDING SITE FOR RESIDUE CL H 1023
30DC3SOFTWAREVAL H:152BINDING SITE FOR RESIDUE CL H 1026
31DC4SOFTWAREPHE H:166 , PRO H:167 , VAL H:169 , SER H:177 , LEU H:178 , SER H:179 , GLN L:160 , SER L:162 , SER L:176 , THR L:178BINDING SITE FOR RESIDUE TRS H 1040
32DC5SOFTWARESER L:121 , ASP L:122 , GLU L:123BINDING SITE FOR RESIDUE SO4 L 1003
33DC6SOFTWAREARG L:85 , ARG L:142BINDING SITE FOR RESIDUE SO4 L 1004
34DC7SOFTWARESER L:27 , TYR L:30BINDING SITE FOR RESIDUE CL L 1011
35DC8SOFTWARELYS L:145 , GLU L:195 , THR L:197BINDING SITE FOR RESIDUE CL L 1012
36DC9SOFTWARELYS H:143 , GLN L:124 , THR L:129BINDING SITE FOR RESIDUE CL L 1018
37EC1SOFTWARESER L:63 , GLY L:64 , SER L:65 , THR L:72 , THR L:74BINDING SITE FOR RESIDUE CL L 1020
38EC2SOFTWARETHR L:5 , SER L:7 , SER L:22 , THR L:24BINDING SITE FOR RESIDUE CL L 1024

(-) 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  (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:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SE9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SE9)

(-) Exons   (0, 0)

(no "Exon" information available for 3SE9)

(-) 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:344
 aligned with Q0ED31_9HIV1 | Q0ED31 from UniProtKB/TrEMBL  Length:857

    Alignment length:444
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482    
        Q0ED31_9HIV1     43 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTPLCVTLHCTTAKLTNVTNITNVPNIGNITDEVRNCSFNMTTEIRDKKQKVHALFYKLDIVQIEDKNDSSKYRLINCNTSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNNMRTSMRIGPGQVFYRTGSITGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  486
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhhhee.......ee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee.----------------------------------------------------------------------------.eeee............eeee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee...---------------------....eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh......---......eeeeeeee..eeee....eeee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3se9 G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTG----------------------------------------------------------------------------GSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSN---------------------GDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIG---MKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113       123|        -         -         -         -         -         -         -       200       210       220       230       240       250       260       270       280       290       300|        -         -  |    331       341       351   ||  362       372       382       392    |  408       418       428       438       448       458       468       478       488    
                                                                                                          124                                                                          198                                                                                                    301                   324                            355|                                     397 407                                                                                     
                                                                                                                                                                                                                                                                                                                                                    357                                                                                                                                 


Chain H from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eee.....eeeeee.hhhhhhheeeeeeeee......eeeeeee.....eee.hhhhhhheeeeee....eeeeee...hhhhheeeeeeeee...........ee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3se9 H    1 QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVNFGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTLIVVSSASTKGPSVFPLAPSSKSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30     |  39        49   ||   57        67        77     |||84        94      100D||     108       118       128||     140       150       160       170       180       190       200       210     
                                                             35A               52A|                            82A||               100A|||||                          129|                                                                                   
                                                                                52B                             82B|                100B||||                           132                                                                                   
                                                                                                                 82C                 100C|||                                                                                                                 
                                                                                                                                      100D||                                                                                                                 
                                                                                                                                       100E|                                                                                                                 
                                                                                                                                        100F                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains d3se9l1 L:1-107 automated matches                                                                    d3se9l2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3se9 L    1 EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRFSGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20      ||32        42        52        62        72        82        96       106       116       126       136       146       156       166       176       186       196       206        
                                                     27|                                                           91|                                                                                                                      
                                                      30                                                            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 3SE9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SE9)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain G   (Q0ED31_9HIV1 | Q0ED31)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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  Cis Peptide Bonds
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  3se9
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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 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 4oly 4olz 4om0 4om1 4p9h 4rfn 4rfo 4rz8 4xnz 4xvt 4ydj 4ydk 4ydl 4yfl

(-) Related Entries Specified in the PDB File

3ngb ANTIBODY VRC01 ISOLATED FROM ANOTHER DONOR