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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING VRC01-CLASS ANTIBODY N6 IN COMPLEX WITH HIV-1 CLADE G STRAIN X2088 GP120 CORE
 
Authors :  T. Zhou, P. D. Kwong
Date :  20 Sep 16  (Deposition) - 23 Nov 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
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 - HIV-1 CLADE G STRAIN X2088 GP120
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: 293
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: GP120
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: EXTENDED CORE PORTION OF HIV-1 GP120
    Strain: X2088
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY 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 ANTIBODY N6
    Cell Line: 293
    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  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1BU31Ligand/Ion(R,R)-2,3-BUTANEDIOL
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO48Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE G:53 , ARG G:327 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:603binding site for residue SO4 G 512
02AC2SOFTWAREHIS G:216 , HIS G:249 , GLY G:250binding site for residue SO4 G 513
03AC3SOFTWAREASN G:362 , ARG G:469binding site for residue SO4 G 514
04AC4SOFTWARETRP G:112 , VAL G:255 , SER G:375 , TYR G:384 , ARG G:425 , TYR H:54binding site for residue BU3 G 515
05AC5SOFTWARETYR H:27 , THR H:28 , HIS H:32 , TYR H:98binding site for residue SO4 H 301
06AC6SOFTWARESER H:7 , GLY H:8binding site for residue SO4 H 302
07AC7SOFTWAREARG H:96binding site for residue MPD H 303
08AC8SOFTWARELYS H:12 , VAL H:18 , ARG H:19binding site for residue SO4 H 304
09AC9SOFTWARESER L:12 , LYS L:107 , TYR L:140binding site for residue SO4 L 302
10AD1SOFTWARETHR G:462 , ARG L:211binding site for residue SO4 L 303
11AD2SOFTWAREASN G:234 , THR G:236 , SER G:274 , THR G:355A , NAG G:504binding site for Mono-Saccharide NAG G 501 bound to ASN G 234
12AD3SOFTWAREGLU G:87 , ARG G:229 , ASN G:241 , LYS G:267binding site for Mono-Saccharide NAG G 502 bound to ASN G 241
13AD4SOFTWAREGLU G:211 , PRO G:212 , LYS G:252 , VAL G:254 , LEU G:261 , ASN G:262 , CYS G:445 , SER G:447 , NAG G:511binding site for Mono-Saccharide NAG G 503 bound to ASN G 262
14AD5SOFTWAREASN G:276 , NAG G:501 , GLN L:27 , GLY L:28 , VAL L:29 , ASP L:32binding site for Mono-Saccharide NAG G 504 bound to ASN G 276
15AD6SOFTWAREILE G:297 , HIS G:330 , ASN G:332 , ASN G:413 , THR G:415 , NAG G:510binding site for Mono-Saccharide NAG G 505 bound to ASN G 332
16AD7SOFTWARETHR G:355A , ASN G:355C , SER L:26 , GLN L:27binding site for Mono-Saccharide NAG G 506 bound to ASN G 355C
17AD8SOFTWAREASN G:357 , ASP G:463A , GLU G:464binding site for Mono-Saccharide NAG G 507 bound to ASN G 357
18AD9SOFTWARELYS G:117 , THR G:373 , ASN G:386 , SER G:388 , HOH G:605binding site for Mono-Saccharide NAG G 508 bound to ASN G 386
19AE1SOFTWARELYS G:202 , GLN G:203 , ASN G:392 , THR G:394binding site for Mono-Saccharide NAG G 509 bound to ASN G 392
20AE2SOFTWAREASN G:332 , GLU G:412 , ASN G:413 , NAG G:505binding site for Mono-Saccharide NAG G 510 bound to ASN G 413
21AE3SOFTWAREASN G:262 , ASN G:448 , NAG G:503binding site for Mono-Saccharide NAG G 511 bound to ASN G 448
22AE4SOFTWAREASN L:72 , SER L:168 , LYS L:169binding site for Mono-Saccharide NAG L 301 bound to ASN L 72

(-) SS Bonds  (11, 11)

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
10L:23 -L:88
11L: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 5TE4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TE4)

(-) Exons   (0, 0)

(no "Exon" information available for 5TE4)

(-) 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 .ee.....eeee.......hhhhhhhhhheee......eeee....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee............eeee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee......eeeeehhhhhhhhhhhhhhhhhhhhhhh.....eeee......hhhhhheeeee..eeeee............eeeee..ee.eee......eee........eeeeeeeeeeeeee..........eeeeee....hhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5te4 G   45 WEDADTTLFCASDAKAYSTEKHNVWATHACVPTDPDPQEIPLENVTENFNMWKNNMVEQMHEDIISLWDESLKPCVMLTGGSTIKQACPKVTFEPIPIHYCAPAGFAILKCRDEDFNGTGPCKNVSTVQCTHGIKPVVSTQLLLNGSLAKGDIVIRSENLTNNAKVIIVQLNEPVQIVCIRPDIRQAHCNVTRGKWVNITKNVKEQLWKIFNKTTNITFNNTIFNSPAGGDLEITTHSFNCGGEFFYCNTSDLFNETNNENITLQCRIKQIVRMWQRVGQAMYAPPIAGNITCISNITGLLLTRDGVNDTHDKENETFRPTGGDMRDNWRSELYKYKVIKL  491
                                    54        64        74        84        94       104       114       124|      207       217       227       237       247       257       267       277       287       297 ||    332       342       352   ||||357       367       377       387       412       422       432       442       452       462 ||    470       480       490 
                                                                                                         124|                                                                                                  299|                           355A||||                                     395|                                                 463A|                            
                                                                                                          198                                                                                                   325                            355B|||                                      411                                                  463B                            
                                                                                                                                                                                                                                                355C||                                                                                                                           
                                                                                                                                                                                                                                                 355D|                                                                                                                           
                                                                                                                                                                                                                                                  355E                                                                                                                           


Chain H from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               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..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5te4 H    1 RAHLVQSGTAMKKPGASVRVSCQTSGYTFTAHILFWFRQAPGRGLEWVGWIKPQYGAVNFGGGFRDRVTLTRDVYREIAYMDIRGLKPDDTAVYYCARDRSYGDSSWALDAWGQGTTVVVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    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..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5te4 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
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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 5TE4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TE4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TE4)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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5te6 5te7