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(-) Description

Title :  CRYSTAL STRUCTURE OF A VRC01-LINEAGE ANTIBODY, 45-VRC01.H08.F-117225, IN COMPLEX WITH CLADE A/E HIV-1 GP120 CORE
 
Authors :  Y. D. Kwon, Y. Yang, B. Zhang, P. D. Kwong
Date :  14 Jan 15  (Deposition) - 22 Apr 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.21
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Hiv-1, Neutralizing Antibodies, Vrc01-Lineage, Antibody Maturation, Evolutionary Rate, Viral Protein-Immune System-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Wu, Z. Zhang, C. A. Schramm, M. G. Joyce, Y. Do Kwon, T. Zhou, Z. Sheng B. Zhang, S. O'Dell, K. Mckee, I. S. Georgiev, G. Y. Chuang, N. S. Longo, R. M. Lynch, K. O. Saunders, C. Soto, S. Srivatsan, Y. Yang, R. T. Bailer M. K. Louder, J. C. Mullikin, M. Connors, P. D. Kwong, J. R. Mascola, L. Shapiro
Maturation And Diversity Of The Vrc01-Antibody Lineage Over 15 Years Of Chronic Hiv-1 Infection.
Cell(Cambridge, Mass. ) V. 161 470 2015
PubMed-ID: 25865483  |  Reference-DOI: 10.1016/J.CELL.2015.03.004

(-) Compounds

Molecule 1 - CLADE A/E 93TH057 HIV-1 GP120 CORE
    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: RESIDUE 44-492
    Gene: HIV-1 ENV
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: CLADE A/E 93TH057
 
Molecule 2 - FAB OF VRC01-LINEAGE ANTIBODY,45-VRC01.H08.F-117225 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PVRC8400
    Expression System Strain: 293F
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: FAB OF VRC01-LINEAGE ANTIBODY,45-VRC01.H08.F-117225 HEAVY CHAIN
    Gene: HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - FAB OF VRC01 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PVRC8400
    Expression System Strain: 293F
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: FAB OF VRC01 LIGHT CHAIN
    Gene: LIGHT CHAIN
    Mutation: YES
    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, 11)

Asymmetric/Biological Unit (1, 11)
No.NameCountTypeFull Name
1NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN G:88BINDING SITE FOR RESIDUE NAG G 501
02AC2SOFTWAREASN G:234 , THR G:236 , SER G:274BINDING SITE FOR RESIDUE NAG G 502
03AC3SOFTWAREHIS G:85 , ASN G:229 , LYS G:231 , ASN G:241 , ASN G:411 , GLY G:412BINDING SITE FOR RESIDUE NAG G 503
04AC4SOFTWAREPRO G:212 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , NAG G:511BINDING SITE FOR RESIDUE NAG G 504
05AC5SOFTWAREGLU G:275 , ASN G:276 , TYR L:28 , GLY L:29 , TYR L:91 , LYS L:171BINDING SITE FOR RESIDUE NAG G 505
06AC6SOFTWAREASN G:80 , GLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLN G:344 , LYS G:348BINDING SITE FOR RESIDUE NAG G 506
07AC7SOFTWAREASN G:295 , GLU G:332BINDING SITE FOR RESIDUE NAG G 507
08AC8SOFTWAREGLU G:83 , HIS G:85 , ASN G:334 , THR G:336 , LYS G:337BINDING SITE FOR RESIDUE NAG G 508
09AC9SOFTWAREGLN G:117 , GLN G:203 , ASN G:386 , THR G:388BINDING SITE FOR RESIDUE NAG G 509
10BC1SOFTWAREGLN G:389 , ASN G:392 , THR G:394 , CYS G:395 , CYS G:410BINDING SITE FOR RESIDUE NAG G 510
11BC2SOFTWAREASN G:262 , SER G:291 , ASN G:448 , NAG G:504BINDING SITE FOR RESIDUE NAG G 511

(-) SS Bonds  (15, 15)

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:100J
11H:99 -H:100E
12H:140 -H:196
13H:216 -L:216
14L:23 -L:88
15L:136 -L:196

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Ser L:7 -Pro L:8
4Asp L:124 -Glu L:125
5Tyr L:142 -Pro L:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S1R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S1R)

(-) Exons   (0, 0)

(no "Exon" information available for 4S1R)

(-) 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......eeee....eeee...hhhhhhhhhhhhhhhhhh....eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee......eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhhhhhhhh.....eeeeeeeee.eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4s1r 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:235
                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........hhhhh....eeee...eeeee........eeee...........eeeeeeeee.......eeee.hhh....eeeeeeee.....eeeeeeeeee.hhh....eeeeeee....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4s1r H    1 QVRLVQSGPQIKTPGASVTISCGTSGYDFMESLINWVRQDIGKGPEWMGWINPRGGGVNYGRRFQGKVTMTRDVSSGTAYLTLRGLTSDDTAKYYCVRGKSCCGGRRYCNGADCFNWDFEHWGQGTLVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||||101       111       121       131       141       151       161       171       181       191       201       211     
                                                                              52A                            82A||               100A|||||100J|||||                                                                                                                    
                                                                                                              82B|                100B|||||100K||||                                                                                                                    
                                                                                                               82C                 100C|||||100L|||                                                                                                                    
                                                                                                                                    100D|||||100M||                                                                                                                    
                                                                                                                                     100E|||| 100N|                                                                                                                    
                                                                                                                                      100F|||  100O                                                                                                                    
                                                                                                                                       100G||                                                                                                                          
                                                                                                                                        100H|                                                                                                                          
                                                                                                                                         100I                                                                                                                          


Chain L from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee......eeeeeee.....eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeee............eee.........eeeeeee.....ee..ee........eeeeee........eeeeeee............ee..ee................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4s1r L    3 VLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYTLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  216
                                    12        22       |34        44        54        64        74        84      ||98       108       118       128|      143       153       163       173       183       193       203       213   
                                                      30|                                                        91|                             128|                                                                                  
                                                       33                                                         96                              134
   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 4S1R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S1R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S1R)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4S1R)

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  Cis Peptide Bonds
    Asp L:124 - Glu L:125   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        A0A0M3KKW9_9 | A0A0M3KKW9: 4s1q 4s1s 4ybl 4yc2 5cd5 5f96 5f9o 5f9w 5fcu 5kjr 5te6 5u6e

(-) Related Entries Specified in the PDB File

4s1q 4s1s