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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC01 IN COMPLEX WITH HIV-1 CLADE C STRAIN ZM176.66 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 :  2.55
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Neutralizing Antibody Vrc01, Hiv Envelope Glycoprotein Gp120, Antibody Antigen, 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 - ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE C
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: ZM176.66
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY VRC01
    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 VRC01
    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  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN G:230 , THR G:232 , PHE G:233 , PRO G:238 , ASN G:240 , THR H:191BINDING SITE FOR MONO-SACCHARIDE NAG G 503 BOUND TO ASN G 230
2AC2SOFTWAREASN G:229 , ASN G:241BINDING SITE FOR MONO-SACCHARIDE NAG G 504 BOUND TO ASN G 241
3AC3SOFTWARELYS G:252 , ASN G:262 , ASN G:377 , CYS G:445 , LYS G:446 , SER G:447 , HOH G:605 , HOH G:606 , HOH G:608BINDING SITE FOR MONO-SACCHARIDE NAG G 501 BOUND TO ASN G 262
4AC4SOFTWAREGLU G:275 , ASN G:276 , TYR L:28 , GLY L:29 , SER L:30 , TYR L:91BINDING SITE FOR MONO-SACCHARIDE NAG G 502 BOUND TO ASN G 276
5AC5SOFTWAREGLU G:335 , ASN G:339 , ASN G:392 , NAG G:507BINDING SITE FOR MONO-SACCHARIDE NAG G 508 BOUND TO ASN G 339
6AC6SOFTWAREGLN G:114 , LYS G:117 , ASN G:386 , THR G:388 , HOH G:623BINDING SITE FOR MONO-SACCHARIDE NAG G 505 BOUND TO ASN G 386
7AC7SOFTWAREASN G:392 , NAG G:508BINDING SITE FOR MONO-SACCHARIDE NAG G 507 BOUND TO ASN G 392
8AC8SOFTWARETHR G:394 , ASN G:396BINDING SITE FOR MONO-SACCHARIDE NAG G 506 BOUND TO ASN G 396

(-) 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
8H:22 -H:92
9H:32 -H:98
10H:140 -H:196
11H:216 -L:216
12L:23 -L:88
13L: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 4LST)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LST)

(-) 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:339
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee........hhhhhhhhhhh.........eee....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eee..............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh.........eeeeeeeee.eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lst G   44 VWKEAKTTLFCASDAKAYEREVHNVWATHACVPTDPNPQEMALGNVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTGGSTVTQACPKVSFDPIPIHYCAPAGYAILKCNNETFEGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAKEEIVIRSENLTDNAKTIIVHLKESVEIVCTRPGDTRQAHCNISEEKWNKTLQKVSKILQEHFPNKAIKFEPHSGGDLEITTHSFNCRGEFFYCNTTKLFNGTYNSSNTTITLPCRIKQIVNMWQGVGRAMYAPPIKGNITCKSIITGLLLTRDGGNDDNDTETFRPGGGDMRDNWRSELYKYKVVEIK  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296   ||  330       340       350    || 361       371       381       391     ||413       423       433       443       453       463       473       483         
                                                                                                          124|                                                                                                   300|                           355|                                     397|                                                                                  
                                                                                                           198                                                                                                    325                            357                                      410                                                                                  


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......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...........ee...eeeee........eeeee.........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4lst H    1 QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVSSPSTKGPSVFPLAPSSKSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       134       144       154       164       174       184       194       204       214  
                                                                              52A                            82A||               100A|||                           130|                                                                                   
                                                                                                              82B|                100B||                            133                                                                                   
                                                                                                               82C                 100C|                                                                                                                  
                                                                                                                                    100D                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains d4lstl1 L:1-107 automated matches                                                                    d4lstl2 L:108-216 automated matches                                                                           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..hhhhhh..eeeeeeeeeee.....eeeeee........ee............eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4lst L    1 EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC  216
                                    10        20        30|       42        52        62        72        82        96       106       116       126       136       146       156       166       176       186       196       206       216
                                                        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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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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    Tyr L:142 - Pro L:143   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        R4GRV3_9HIV1 | R4GRV3: 4jan 5f6j

(-) Related Entries Specified in the PDB File

3ngb 3se8 3se9 4j6r 4jb9 4jpv 4jpw