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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING VRC01-CLASS ANTIBODY N6 IN COMPLEX WITH HIV-1 CLADE C STRAIN DU172.17 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 :  2.15
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 - 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 2 - 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
 
Molecule 3 - 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
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : GHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY H:157 , ALA H:158 , LEU H:159 , THR H:160 , SER H:161 , HOH H:457 , ASP L:17 , ARG L:18 , THR L:20 , HOH L:433binding site for residue EPE H 301
02AC2SOFTWARELEU H:141 , VAL H:169 , SER H:179 , HOH H:431 , HOH H:480 , THR L:178 , HOH L:450binding site for residue EDO H 302
03AC3SOFTWAREGLU H:46 , TRP H:47 , HOH H:415 , HOH H:438 , GLN L:96binding site for residue EDO H 303
04AC4SOFTWAREGLN L:37 , HIS L:38 , LYS L:39 , ARG L:42 , ALA L:43binding site for residue EDO L 302
05AC5SOFTWAREGLN L:37 , LYS L:45 , PRO L:59 , PHE L:62 , HOH L:406binding site for residue EDO L 303
06AC6SOFTWARETYR L:186 , GLY L:212 , GLU L:213binding site for residue EDO L 304
07AC7SOFTWARELEU G:52 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423binding site for residue EPE G 508
08AC8SOFTWAREARG G:425 , MET G:426 , GLY G:429 , GLY G:431binding site for residue EDO G 509
09AC9SOFTWAREASN G:276 , LEU G:277 , ASN G:279 , LYS G:282 , ILE G:284 , ARG G:456binding site for residue EDO G 510
10AD1SOFTWAREASN G:234 , THR G:236 , PHE G:274binding site for Mono-Saccharide NAG G 501 bound to ASN G 234
11AD2SOFTWAREVAL G:85 , ASN G:229 , LYS G:231 , ASN G:241 , SER G:243binding site for Mono-Saccharide NAG G 502 bound to ASN G 241
12AD3SOFTWAREASN G:262 , ARG G:379 , CYS G:445 , LYS G:446 , SER G:447 , NAG G:507binding site for Mono-Saccharide NAG G 503 bound to ASN G 262
13AD4SOFTWAREGLU G:268 , GLU G:269 , VAL G:270 , ASN G:289 , GLU G:290 , ARG G:344binding site for Mono-Saccharide NAG G 504 bound to ASN G 289
14AD5SOFTWAREASN G:295 , ASN G:332 , ASN G:413 , LYS G:446binding site for Mono-Saccharide NAG G 505 bound to ASN G 295
15AD6SOFTWAREGLY G:222 , ASN G:392 , THR G:394 , TYR G:395 , ILE G:491binding site for Mono-Saccharide NAG G 506 bound to ASN G 392
16AD7SOFTWAREASN G:262 , ASN G:448 , NAG G:503binding site for Mono-Saccharide NAG G 507 bound to ASN G 448
17AD8SOFTWARESER H:161 , GLY H:162 , THR H:183 , THR L:20 , ILE L:21 , ASN L:22 , ASN L:72 , HOH L:402 , HOH L:409binding 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
8H:22 -H:92
9H:140 -H:196
10H:216 -L:214
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 5TE7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TE7)

(-) Exons   (0, 0)

(no "Exon" information available for 5TE7)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee........hhhhhhhhhhh.........ee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee......eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee..............eeeeeeee..eee......eee........eeeeeeeeeeeeee.......eeeeee....hhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5te7 G   45 WKEAKTTLFCASDAKAHKEEVHNIWATHACVPTDPNPQEIVLKNVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTGGSAVTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVVIRFENLTNNAKIIIVHLNESVEINCTRPSNDIRQAHCNISRKKWNTTLQRVKEKLKEKFPNKTIQFAPSSGGDLEITTHSFNCRGEFFYCYTSDLFNSTYMGGANITLQCRIKQIIRMWQGVGQAMYAPPIAGNITCKSNITGLLLTRDGGKKNDTETFRPGGGDMRDNWRSELYKYKVVEI  491
                                    54        64        74        84        94       104       114       124|      207       217       227       237       247       257       267       277       287       297   ||  330       340       350    || 361       371       381       391    || 414       424       434       444       454     ||465       475       485      
                                                                                                         124|                                                                                                    301|                           355|                                    396|                                               460|                             
                                                                                                          198                                                                                                     325                            357                                     410                                                462                             


Chain H from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee..hhhh.eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5te7 H    1 RAHLVQSGTAMKKPGASVRVSCQTSGYTFTAHILFWFRQAPGRGLEWVGWIKPQYGAVNFGGGFRDRVTLTRDVYREIAYMDIRGLKPDDTAVYYCARDRSYGDSSWALDAWGQGTTVVVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121       131       141       151       161       171       181       191       201       211     
                                                                              52A                            82A||               100A||||                                                                                                                    
                                                                                                              82B|                100B|||                                                                                                                    
                                                                                                               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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5te7 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)
  - → 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 5TE7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TE7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TE7)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

5te4 5te6