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(-) Description

Title :  CRYSTAL STRUCTURE OF MANDRILL SAMHD1 (AMINO ACID RESIDUES 1-114) BOUND TO VPX ISOLATED FROM MANDRILL AND HUMAN DCAF1 (AMINO ACID RESIDUES 1058-1396)
 
Authors :  D. Schwefel, V. C. Boucherit, E. Christodoulou, P. A. Walker, J. P. Stoy K. N. Bishop, I. A. Taylor
Date :  20 Feb 15  (Deposition) - 22 Apr 15  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Viral Protein, Siv, Accessory Protein, Retroviral Restriction Factor, Ubiquitylation, Proteasomal Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Schwefel, V. C. Boucherit, E. Christodoulou, P. A. Walker, J. P. Stoye, K. N. Bishop, I. A. Taylor
Molecular Determinants For Recognition Of Divergent Samhd1 Proteins By The Lentiviral Accessory Protein Vpx.
Cell Host Microbe. V. 17 489 2015
PubMed-ID: 25856754  |  Reference-DOI: 10.1016/J.CHOM.2015.03.004

(-) Compounds

Molecule 1 - PROTEIN VPRBP
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPTRIEX-6
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentWD40-REPEAT DOMAIN, RESIDUES 1058-1396
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDCAF1, DDB1- AND CUL4-ASSOCIATED FACTOR 1, HIV-1 VPR-BINDING PROTEIN, VPRBP, SERINE/THREONINE-PROTEIN KINASE VPRBP, VPR-INTERACTING PROTEIN
 
Molecule 2 - VPX PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET49B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA2
    Expression System Vector TypePLASMID
    Organism ScientificSIMIAN IMMUNODEFICIENCY VIRUS
    Organism Taxid11723
    StrainMND-2
    Variant5440
 
Molecule 3 - SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET52B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA2
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN, UNP 1-114
    Organism CommonMANDRILL
    Organism ScientificMANDRILLUS SPHINX
    Organism Taxid9561
    SynonymSAMHD1, SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:35 , HIS B:78 , CYS B:83 , HOH B:2002BINDING SITE FOR RESIDUE ZN B1086

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AJA)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:1158 -Pro A:1159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AJA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AJA)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.........eeeeee.....eeeeee...eeeeee.....eeeeee.......eeee.....eeeee.......eeeee......eeeee....eeee......eeeeee..eeeeee.....eeeee..............ee.....eeee..eeee....eeeee..........ee.....eeee..eeee.....eeee.hhhh.eeeee.....eeeeeee.....eeeeeeeee.....eeeeee...eeeeeee.....eeeeeee..........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5aja A 1075 LIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQAKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQ 1392
                                  1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314||    1335      1345      1355      1365      1375      1385       
                                                                                                                                                                                                                                                                         1315|                                                                 
                                                                                                                                                                                                                                                                          1327                                                                 

Chain B from PDB  Type:PROTEIN  Length:84
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                5aja B    2 AERAPEAPEGAGEVGLEQWLETSLERINREARLHFHPEFLFRLWNTCVEHWHDRHQRSLDYAKYRYLLLMHKAMYTHMQQGCPC   85
                                    11        21        31        41        51        61        71        81    

Chain C from PDB  Type:PROTEIN  Length:94
                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                5aja C    1 MQQADSDQPSKRPRFDDSPRTPPGVELHPDYKTWGPEQVCFFLRRGGFGEPALLKNIRENKITGALLPCLDESHFENSLGERKKLLSYIQRSGQ  109
                                    10        20 ||     41        51        61        71        81      ||95       105    
                                                22|                                                    88|                
                                                 34                                                     93                

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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 5AJA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCAF1_HUMAN | Q9Y4B63wa0 4cc9 4p7i 4pxw 4z8l 5jk7
UniProtKB/TrEMBL
        H6WEA4_MANSP | H6WEA44z8l
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(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5AJA)