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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING VRC01-CLASS ANTIBODY N6 IN COMPLEX WITH HIV-1 CLADE AE STRAIN 93TH057 GP120 CORE
 
Authors :  T. Zhou, P. D. Kwong
Date :  20 Sep 16  (Deposition) - 16 Nov 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Hiv-1, Vrc01-Class Antibody, N6, Cd4-Binding Site, Gp120, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Huang, B. H. Kang, E. Ishida, T. Zhou, T. Griesman, Z. Sheng, F. Wu, N. A. Doria-Rose, B. Zhang, K. Mckee, S. O'Dell, G. Y. Chuang, A. Druz, I. S. Georgiev, C. A. Schramm, A. Zheng, M. G. Joyce, M. Asokan, A. Ransier, S. Darko, S. A. Migueles, R. T. Bailer, M. K. Louder, S. M. Alam, R. Parks, G. Kelsoe, T. Von Holle, B. F. Haynes, D. C. Douek, V. Hirsch, M. S. Seaman, L. Shapiro, J. R. Mascola, P. D. Kwong, M. Connors
Identification Of A Cd4-Binding-Site Antibody To Hiv That Evolved Near-Pan Neutralization Breadth.
Immunity V. 45 1108 2016
PubMed-ID: 27851912  |  Reference-DOI: 10.1016/J.IMMUNI.2016.10.027

(-) Compounds

Molecule 1 - CLADE A/E 93TH057 HIV-1 GP120 CORE
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: HIV-1 ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - HEAVY CHAIN OF N6
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - LIGHT CHAIN OF N6
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    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  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU G:52 , GLN G:103 , ASP G:107 , TYR G:217 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423binding site for residue EPE G 511
02AC2SOFTWAREASN G:234 , THR G:236 , SER G:274 , NAG G:504binding site for Mono-Saccharide NAG G 501 bound to ASN G 234
03AC3SOFTWAREGLU G:83 , ASN G:229 , ASN G:241binding site for Mono-Saccharide NAG G 502 bound to ASN G 241
04AC4SOFTWAREPRO G:212 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , NAG G:510 , HOH G:603binding site for Mono-Saccharide NAG G 503 bound to ASN G 262
05AC5SOFTWAREASN G:276 , NAG G:501 , HOH G:638 , GLN L:27 , GLY L:28 , VAL L:29 , ASP L:32 , VAL L:90binding site for Mono-Saccharide NAG G 504 bound to ASN G 276
06AC6SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289binding site for Mono-Saccharide NAG G 505 bound to ASN G 289
07AC7SOFTWAREASN G:295 , TYR G:330 , GLU G:332 , HOH G:616 , HOH G:625binding site for Mono-Saccharide NAG G 506 bound to ASN G 295
08AC8SOFTWAREPRO G:81 , GLN G:82 , GLU G:83 , ASN G:334 , LYS G:337binding site for Mono-Saccharide NAG G 507 bound to ASN G 334
09AC9SOFTWAREMET G:373 , ASN G:386binding site for Mono-Saccharide NAG G 508 bound to ASN G 386
10AD1SOFTWAREASN G:392binding site for Mono-Saccharide NAG G 509 bound to ASN G 392
11AD2SOFTWARELYS G:252 , ASN G:262 , ASN G:448 , NAG G:503binding site for Mono-Saccharide NAG G 510 bound to ASN G 448
12AD3SOFTWARETHR L:20 , ASN L:72 , LYS L:169binding site for Mono-Saccharide NAG L 301 bound to ASN L 72

(-) 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 5TE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TE6)

(-) Exons   (0, 0)

(no "Exon" information available for 5TE6)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhhhee.......eee....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhhhhhhh....eeeeeeee..eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5te6 G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348      |359       369       379       389       411       421       431       441       451       461       471       481       491 
                                                                                                          124|                                                                                                    301|                            355|                                     397|                                                                                  
                                                                                                           198                                                                                                     324                             357                                      410                                                                                  


Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee............eeeeeeee.....eeee.hhh....eee...ee.....eeeeeee..hhhhhh...eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5te6 H    1 RAHLVQSGTAMKKPGASVRVSCQTSGYTFTAHILFWFRQAPGRGLEWVGWIKPQYGAVNFGGGFRDRVTLTRDVYREIAYMDIRGLKPDDTAVYYCARDRSYGDSSWALDAWGQGTTVVVSAASTKGPSVFPLAPSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121     ||132       142       152       162       172       182       192       202       212   
                                                                              52A                            82A||               100A||||                        127|                                                                                      
                                                                                                              82B|                100B|||                         129                                                                                      
                                                                                                               82C                 100C||                                                                                                                  
                                                                                                                                    100D|                                                                                                                  
                                                                                                                                     100E                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5te6 L    1 YIHVTQSPSSLSVSIGDRVTINCQTSQGVGSDLHWYQHKPGRAPKLLIHHTSSVEDGVPSRFSGSGFHTSFNLTISDLQADDIATYYCQVLQFFGRGSRLHIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90||     104       114       124       134       144       154       164       174       184       194       204       214
                                                                                                                     91|                                                                                                                      
                                                                                                                      96
   Legend:   → Mismatch (orange background)
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  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 5TE6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TE6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TE6)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5TE6)

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 Related Entries

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

UniProtKB/TrEMBL
        A0A0M3KKW9_9 | A0A0M3KKW9: 4s1q 4s1r 4s1s 4ybl 4yc2 5cd5 5f96 5f9o 5f9w 5fcu 5kjr 5u6e

(-) Related Entries Specified in the PDB File

5te4 5te7