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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC03 IN COMPLEX WITH HIV-1 GP120
 
Authors :  P. D. Kwong, T. Zhou
Date :  10 Jun 11  (Deposition) - 10 Aug 11  (Release) - 15 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Hiv, Gp120, Antibody, Vrc03, 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 TRUNCATIONS
    Gene: GP120
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: 93TH057
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY VRC03
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: CMVR DERIVED PLASMIDS FOR IGG1
    Expression System Strain: 293F
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: ANTIGEN BINDING FRAGEMENT OF ANTIBODY HEAVY CHAIN
    Gene: ANTIBODY VRC03 HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - LIGHT CHAIN OF ANTIBODY VRC03
    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 VRC03 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  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO48Ligand/IonSULFATE ION
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU G:87 , ASN G:88 , HOH G:596BINDING SITE FOR RESIDUE NAG G 588
02AC2SOFTWAREASN G:234 , HOH G:599 , HOH G:634BINDING SITE FOR RESIDUE NAG G 734
03AC3SOFTWAREASN G:229 , ASN G:241 , HOH G:542 , HOH G:544 , HOH G:636BINDING SITE FOR RESIDUE NAG G 741
04AC4SOFTWAREHOH G:168 , ASN G:262 , ARG G:379 , CYS G:445 , SER G:447 , HOH G:511 , HOH G:566 , HOH G:614 , NAG G:948BINDING SITE FOR RESIDUE NAG G 762
05AC5SOFTWAREGLU G:275 , ASN G:276 , HOH G:568 , HOH H:457 , SO4 H:1001 , ALA L:32 , ASP L:50 , PHE L:91 , HOH L:455BINDING SITE FOR RESIDUE NAG G 776
06AC6SOFTWAREGLU G:269 , ILE G:270 , ASN G:289 , LYS G:348 , HOH G:592 , HOH G:607 , SO4 G:1002BINDING SITE FOR RESIDUE NAG G 789
07AC7SOFTWAREASN G:295 , THR G:297 , TYR G:330 , GLU G:332 , HOH G:573 , HOH G:667BINDING SITE FOR RESIDUE NAG G 795
08AC8SOFTWAREPRO G:79 , ASN G:80 , ASN G:334 , LYS G:337 , HOH G:519BINDING SITE FOR RESIDUE NAG G 834
09AC9SOFTWAREASN G:386 , THR G:388 , HOH G:635BINDING SITE FOR RESIDUE NAG G 886
10BC1SOFTWAREGLN G:389 , ASN G:392 , CYS G:395 , GLY G:409 , CYS G:410BINDING SITE FOR RESIDUE NAG G 892
11BC2SOFTWARELYS G:252 , ASN G:262 , SER G:291 , ASN G:448 , HOH G:572 , HOH G:647 , NAG G:762BINDING SITE FOR RESIDUE NAG G 948
12BC3SOFTWAREASN G:474 , LYS G:476 , ARG G:480 , HOH G:560BINDING SITE FOR RESIDUE SO4 G 1000
13BC4SOFTWARELYS G:290 , LYS G:340 , GLN G:344 , NAG G:789BINDING SITE FOR RESIDUE SO4 G 1002
14BC5SOFTWAREASN G:279 , NAG G:776 , GLY H:100B , ASP H:100C , PHE H:100D , PRO H:100E , HOH H:237 , HOH H:342 , HOH H:456 , HOH H:457 , PHE L:91BINDING SITE FOR RESIDUE SO4 H 1001
15BC6SOFTWAREGLY H:65 , ARG H:66 , VAL H:67 , SER H:68 , GLU H:81 , SER H:82ABINDING SITE FOR RESIDUE SO4 H 1004
16BC7SOFTWAREASN G:474 , LYS H:52 , HOH H:626BINDING SITE FOR RESIDUE SO4 H 1005
17BC8SOFTWARESER H:127 , ALA H:137 , PHE L:116 , ILE L:117 , PHE L:118BINDING SITE FOR RESIDUE EDO H 1008
18BC9SOFTWAREVAL H:150 , THR H:151 , VAL H:152 , THR H:165 , HOH H:255 , HOH H:280 , HOH H:501 , HOH H:636BINDING SITE FOR RESIDUE TRS H 1009
19CC1SOFTWAREPRO H:41 , THR H:87 , ALA H:88 , GLU H:89 , HOH H:236 , HOH H:607BINDING SITE FOR RESIDUE EDO H 1010
20CC2SOFTWAREARG L:45 , PRO L:59 , ARG L:61 , HOH L:276 , HOH L:486BINDING SITE FOR RESIDUE SO4 L 1003
21CC3SOFTWARESER L:121 , ASP L:122 , GLU L:123 , HOH L:533BINDING SITE FOR RESIDUE SO4 L 1006
22CC4SOFTWARESER L:67 , GLY L:68 , ARG L:108 , THR L:109 , HOH L:271 , HOH L:280 , HOH L:418BINDING SITE FOR RESIDUE SO4 L 1007

(-) 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:98 -H:100A
11H:140 -H:196
12L:23 -L:88
13L: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 3SE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SE8)

(-) Exons   (0, 0)

(no "Exon" information available for 3SE8)

(-) 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......eeee....eeee...hhhhhhhhhhhhhhhhhhh...eeee.----------------------------------------------------------------------------.eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee...----------------------...eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhhhhhhhh.--......eeeeeeee..eeee....eeee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3se8 G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTG----------------------------------------------------------------------------GSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSN----------------------DIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGN--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                    325                           355|                                      398  |                                                                                     
                                                                                                                                                                                                                                                                                                                                                    357                                         407                                                                                     


Chain H from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.hhhh..eeeeeee.........eeeeeee...hhhhheeeeeeee..........eeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3se8 H    1 QVQLVQSGAVIKTPGSSVKISCRASGYNFRDYSIHWVRLIPDKGFEWIGWIKPLWGAVSYARQLQGRVSMTRQLSQDPDDPDWGVAYMEFSGLTPADTAEYFCVRRGSCDYCGDFPWQYWCQGTVVVVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69       76C||||    82|||     89        99 ||||||103       113       123    || 137       147       157       167       177       187       197       207       
                                                                              52A                      76A||||||    82A||               100A|||||                         128|                                                                                 
                                                                                                        76B|||||     82B|                100B||||                          133                                                                                 
                                                                                                         76C||||      82C                 100C|||                                                                                                              
                                                                                                          76D|||                           100D||                                                                                                              
                                                                                                           76E||                            100E|                                                                                                              
                                                                                                            76F|                             100F                                                                                                              
                                                                                                             76G                                                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains d3se8l1 L:1-107 automated matches                                                                     d3se8l2 L:108-213 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..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3se8 L    1 EIVLTQSPGILSLSPGETATLFCKASQGGNAMTWYQKRRGQVPRLLIYDTSRRASGVPDRFVGSGSGTDFFLTINKLDREDFAVYYCQQFEFFGLGSELEVHRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20      ||31        41        51        61        71        81        91|      105       115       125       135       145       155       165       175       185       195       205        
                                                     27|                                                            91|                                                                                                                     
                                                      29                                                             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 3SE8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SE8)

(-) 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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  Q0ED31_9HIV1 | Q0ED31
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 Related Entries

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

UniProtKB/TrEMBL
        Q0ED31_9HIV1 | Q0ED31: 3ngb 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 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 THE SAME DONOR