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(-) Description

Title :  HIV-1 NEF PROTEIN IN COMPLEX WITH SINGLE DOMAIN ANTIBODY SDAB19 AND AN ENGINEERED HCK SH3 DOMAIN
 
Authors :  M. Geyer, S. Lulf
Date :  12 Feb 14  (Deposition) - 26 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Sh3 Domain, Immunglobolin Fold, Antibodies, Epitopes, Hiv Antibodies, Hiv Accessory Proteins, Pxxp Motif, Complementarity Determining Regions, Transferase-Apoptosis-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lulf, J. Matz, M. C. Rouyez, A. Jarviluoma, K. Saksela, S. Benichou, M. Geyer
Structural Basis For The Inhibition Of Hiv-1 Nef By A High-Affinity Binding Single-Domain Antibody.
Retrovirology V. 11 24 2014
PubMed-ID: 24620746  |  Reference-DOI: 10.1186/1742-4690-11-24

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE HCK
    Chains: A
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PGEX-2T
    Fragment: SH3 DOMAIN, UNP RESIDUES 77-138
    Gene: HCK
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEMATOPOIETIC CELL KINASE, HEMOPOIETIC CELL KINASE, P59- HCK/P60-HCK, P59HCK, P61HCK
 
Molecule 2 - PROTEIN NEF
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PGEX-4T1
    Fragment: NEF PROTEIN, UNP RESIDUES 45-210
    Gene: NEF
    Mutation: YES
    Organism Common: HIV-1
    Organism Taxid: 11685
    Synonym: 3'ORF, NEGATIVE FACTOR, F-PROTEIN, C-TERMINAL CORE PROTEIN
 
Molecule 3 - SINGLE DOMAIN ANTIBODY SDAB19
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PGEX-4T1
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4ORZ)

(-) Sites  (0, 0)

(no "Site" information available for 4ORZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ORZ)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly B:134 -Pro B:135
2Pro B:154 -Glu B:155
3Gly C:28 -Phe C:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ORZ)

(-) 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 A from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains d4orza_ A: automated matches                             SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..................eeeeee....eeeeee.....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4orz A  81 IIVVALYDYYSPFSWDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARV 136
                                    90       100       110       120       130      


Chain B from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains d4orzb_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.......................eeeee......hhhhh.eeeee.hhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4orz B  71 GFPVRPQVPLRPMTYKAALDISHFLKEKGGLEGLIWSQRRQEILDLWIYHTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVEPEKVDAEKEVLVWRFDSKLAFHHMARELHPEYYK 208
                                    80        90       100       110       120       130       140       150      |181       191       201       
                                                                                                                157|                             
                                                                                                                 179                             


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains d4orzc_ C: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee....eeeeeee........eeeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4orz C   5 QLVESGGGLVQAGGSLRLFCAASGFTFGTSNMAWLRQAPGKRREWVALITISGYTDYADSVKDRFTISRDNAKNTVSLQMNSLKPEDTAIYFCARRVGSEYDLWGQGTQVTVSS 118
                                    14        24        34        44        54        64        74        84        94       104       114
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 77)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly B:134 - Pro B:135   [ RasMol ]  
    Gly C:28 - Phe C:29   [ RasMol ]  
    Pro B:154 - Glu B:155   [ RasMol ]  
 

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  NEF_HV1A2 | P03407
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 Related Entries

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

UniProtKB/Swiss-Prot
        HCK_HUMAN | P08631: 1ad5 1bu1 1qcf 2c0i 2c0o 2c0t 2hck 2hk5 2oi3 2oj2 3hck 3nhn 3rbb 3rea 3reb 3vry 3vrz 3vs0 3vs1 3vs2 3vs3 3vs4 3vs5 3vs6 3vs7 4hck 4lud 4lue 4u5w 5hck
        NEF_HV1A2 | P03407: 3rbb 3rea 3reb 4u1k 4u1l 4u1m 4u1n 4u5w

(-) Related Entries Specified in the PDB File

3rbb HIV-1 NEF PROTEIN IN COMPLEX WITH ENGINEERED HCK SH3 DOMAIN
3rea HIV-1 NEF PROTEIN IN COMPLEX WITH ENGINEERED HCK-SH3 DOMAIN