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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY 3BNC117 IN COMPLEX WITH HIV-1 GP120
 
Authors :  T. Zhou, S. Moquin, P. D. Kwong
Date :  19 Mar 13  (Deposition) - 17 Apr 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.83
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Hiv, Gp120, Cd4-Binding Site, 3Bnc117, Neutralization, Vaccine, Antibody, Envelope Protein, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Klein, R. Diskin, J. F. Scheid, C. Gaebler, H. Mouquet, I. S. Georgiev, M. Pancera, T. Zhou, R. B. Incesu, B. Z. Fu, P. N. Gnanapragasam, T. Y. Oliveira, M. S. Seaman, P. D. Kwong, P. J. Bjorkman, M. C. Nussenzweig
Somatic Mutations Of The Immunoglobulin Framework Are Generally Required For Broad And Potent Hiv-1 Neutralization.
Cell(Cambridge, Mass. ) V. 153 126 2013
PubMed-ID: 23540694  |  Reference-DOI: 10.1016/J.CELL.2013.03.018

(-) Compounds

Molecule 1 - HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP D AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Strain: HEK293F CELL
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY 3BNC117
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    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 3BNC117
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Strain: HEK293F
    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  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN G:234 , THR G:236 , ILE G:272 , ILE G:277BINDING SITE FOR RESIDUE NAG G 501
02AC2SOFTWAREHIS G:85 , ASN G:229 , ASN G:241BINDING SITE FOR RESIDUE NAG G 502
03AC3SOFTWARELYS G:252 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , NAG G:510 , HOH G:609 , HOH G:648BINDING SITE FOR RESIDUE NAG G 503
04AC4SOFTWAREGLU G:275 , ASN G:276 , GLY L:27 , TYR L:32 , TYR L:91BINDING SITE FOR RESIDUE NAG G 504
05AC5SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , LYS G:348BINDING SITE FOR RESIDUE NAG G 505
06AC6SOFTWAREASN G:295 , GLU G:332 , HOH G:601 , HOH G:649BINDING SITE FOR RESIDUE NAG G 506
07AC7SOFTWAREGLU G:83 , HIS G:85 , ASN G:334 , THR G:336 , LYS G:337 , EDO G:513BINDING SITE FOR RESIDUE NAG G 507
08AC8SOFTWARETHR G:372 , ASN G:386 , THR G:388BINDING SITE FOR RESIDUE NAG G 508
09AC9SOFTWAREASN G:392 , CYS G:395 , GLY G:409BINDING SITE FOR RESIDUE NAG G 509
10BC1SOFTWARESER G:291 , ASN G:448 , NAG G:503BINDING SITE FOR RESIDUE NAG G 510
11BC2SOFTWARELEU G:52 , GLN G:103 , ASP G:107 , ARG G:327 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:626BINDING SITE FOR RESIDUE EPE G 511
12BC3SOFTWAREGLU G:381 , PHE G:382 , ILE G:420 , LYS G:421 , ALA G:436 , PRO G:437 , PRO G:438BINDING SITE FOR RESIDUE EDO G 512
13BC4SOFTWAREGLU G:293 , ASN G:334 , LYS G:337 , NAG G:507BINDING SITE FOR RESIDUE EDO G 513
14BC5SOFTWAREASP G:368 , ASN G:425 , LYS H:53BINDING SITE FOR RESIDUE EDO G 514
15BC6SOFTWARESER H:161 , THR L:20 , ARG L:65 , GLU L:70 , ASN L:72 , LYS L:169BINDING SITE FOR RESIDUE NAG L 301
16BC7SOFTWARETRP H:47 , GLU L:96 , VAL L:98BINDING SITE FOR RESIDUE EDO L 302

(-) 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
1Glu G:268 -Glu G:269
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JPV)

(-) 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.......ee.....eeee.hhhhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee........eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhh..eee..eeeee.hhhhhhhhhh.....eeeeeeee..eee......eee........eeeeeeeeeeeeee.......eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4jpv G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRTENITDNAKTIIVHLNKSVEINCTRPSNGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGENNSTEIFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296     ||327       337       347       358       368       378       388       409       419       429       439       449       459 ||    470       480       490  
                                                                                                          124|                                                                                                     302|                            355|                                    396|                                                  461|                             
                                                                                                           198                                                                                                      324                             357                                     408                                                   463                             


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...eee.....eeeeeeeee.hhhhheeeeeee.....eeeeeee......ee..........eeeee......eeeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee....eeeeeeeeee.....eeee.........ee...ee.....eeeeeeeeehhhhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4jpv H    1 QVQLLQSGAAVTKPGASVRVSCEASGYNIRDYFIHWWRQAPGQGLQWVGWINPKTGQPNNPRQFQGRVSLTRHASWDFDTYSFYMDLKALRSDDTAVYFCARQRSDYWDFDVWGSGTQVTVSSASTKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69  ||||  75       82C        92      100B       110       120      |137       147       157       167       177       187       197       207      
                                                                              52A                 71A|||         82A||               100A|                        127|                                                                              
                                                                                                   71B||          82B|                100B                         135                                                                              
                                                                                                    71C|           82C                                                                                                                              
                                                                                                     71D                                                                                                                                            


Chain L from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                             
               SCOP domains d4jpvl1 L:1-107 automated matches                                                                  d4jpvl2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee......eeeeee....eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee....eee..........eee..hhhhhh..eeeeeeeeeee....eeeeeee...ee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4jpv L    1 DIQMTQSPSSLSASVGDTVTITCQANGYLNWYQQRRGKAPKLLIYDGSKLERGVPSRFSGRRWGQEYNLTINNLQPEDIATYFCQVYEFVVPGTRLDLKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20      ||34        44        54        64        74        84      ||98       108       118       128       138       148       158       168       178       188       198       208    
                                                     27|                                                         91|                                                                                                                    
                                                      32                                                          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  (2, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  Q0ED31_9HIV1 | Q0ED31
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 Related Entries

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

UniProtKB/TrEMBL
        Q0ED31_9HIV1 | Q0ED31: 3ngb 3se8 3se9 3tgt 3u7y 4dko 4dkp 4dkq 4dkr 4dku 4dkv 4dvs 4dvt 4dvv 4dvw 4dvx 4h8w 4i54 4jb9 4jdt 4jkp 4jpw 4lsp 4lsq 4lsr 4lsu 4olu 4olv 4olw 4olx 4oly 4olz 4om0 4om1 4p9h 4rfn 4rfo 4rz8 4xnz 4xvt 4ydj 4ydk 4ydl 4yfl

(-) Related Entries Specified in the PDB File

3ngb 3se8 3se9 4gw4 4jpw