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(-) Description

Title :  CRYSTAL STRUCTURE OF CHIMERIC GERM-LINE PRECURSOR OF NIH45-46 FAB IN COMPLEX WITH GP120 OF 93TH057 HIV-1
 
Authors :  L. Scharf, R. Diskin, P. J. Bjorkman
Date :  25 Feb 13  (Deposition) - 20 Mar 13  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.26
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Ig Fold, Anti Hiv, Antibody, Immune System Complex, Viral Protein- Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Scharf, A. P. West, H. Gao, T. Lee, J. F. Scheid, M. C. Nussenzweig, P. J. Bjorkman, R. Diskin
Structural Basis For Hiv-1 Gp120 Recognition By A Germ-Line Version Of A Broadly Neutralizing Antibody.
Proc. Natl. Acad. Sci. Usa V. 110 6049 2013
PubMed-ID: 23524883  |  Reference-DOI: 10.1073/PNAS.1303682110

(-) Compounds

Molecule 1 - GP120
    Chains: G
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Strain: HI5
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Fragment: GP120 CORE
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: 93TH057
 
Molecule 2 - FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HEK293-6E
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: NIH45-46 GERM-LINE HEAVY CHAIN, IG GAMMA-1 CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HEK293-6E
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: NIH45-46 LIGHT CHAIN
    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, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN G:474 , LYS G:476 , ARG G:480BINDING SITE FOR RESIDUE SO4 G 601
2AC2SOFTWAREPRO G:212 , LYS G:252 , ASN G:262 , ASN G:377 , CYS G:445 , VAL G:446 , SER G:447BINDING SITE FOR RESIDUE NAG G 602

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1G:54 -G:74
2G:65 -G:115
3G:119 -G:205
4G:218 -G:247
5G:228 -G:239
6G:296 -G:331
7G:378 -G:445
8G:385 -G:418
9H:22 -H:92
10H:144 -H:200
11L:23 -L:86
12L:130 -L:190

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:150 -Pro H:151
2Glu H:152 -Pro H:153
3Ser L:7 -Pro L:8
4Tyr L:136 -Pro L:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JDT)

(-) 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 ..ee.....eeee.......hhhhhhhhhhhee.......ee.....eeee...hhhhhhhhhhhhhhhhhhh...eee....eee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhh.....eee......hhhhhheeeee..eeeee......hhhhh..eeeeeeeee.eee......eee........eeeeeeeeeeeeee.........eeeee....hhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jdt G  44 VWKDADTTLFCASDAKAHETECHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQCLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCINGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQI 491
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 330       340       350    || 361       371       381       391    || 415       425       435       445       455       465       475       485      
                                                                                                          124|                                                                                                    301|                          355|                                    396|                                                                                
                                                                                                           198                                                                                                     326                           357                                     411                                                                                


Chain H from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee...eeeeeeeeee....eeeee.hhh....eee...ee.....eeeeeeeeehhhhh...eeeeee.hhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jdt H   2 VQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGKYCYYNWDFQHWGQGTLVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLQTYICNVNHKPSNTKVDKRVE 216
                                    11        21        31        41        51 |      60        70        80  |||   87        97 |     107       117       127  ||   145       155       165       175       185       197       207         
                                                                             52A                            82A||              99D                            130|                                                   193|                    
                                                                                                             82B|                                              139                                                    196                    
                                                                                                              82C                                                                                                                            


Chain L from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeee.....eeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeee.........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jdt L   3 VLTQSPATLSLSPGETAIISCRTSQSGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGADYNLSISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 208
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   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 4JDT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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    Tyr L:136 - Pro L:137   [ RasMol ]  
 

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  Q0ED31_9HIV1 | Q0ED31
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 Related Entries

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UniProtKB/TrEMBL
        Q0ED31_9HIV1 | Q0ED31: 3ngb 3se8 3se9 3tgt 3u7y 4dko 4dkp 4dkq 4dkr 4dku 4dkv 4dvs 4dvt 4dvv 4dvw 4dvx 4h8w 4i54 4jb9 4jkp 4jpv 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

4jdv