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(-) Description

Title :  CRYSTAL STRUCTURE OF DCAF1/SIV-MND VPX/MND SAMHD1 NTD TERNARY COMPLEX
 
Authors :  L. M. Koharudin, Y. Wu, G. Calero, J. Ahn, A. M. Gronenborn
Date :  09 Apr 15  (Deposition) - 17 Jun 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Hiv, Antiviral Defense, Viral Protein-Vpx-Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wu, L. M. Koharudin, J. Mehrens, M. Delucia, C. H. Byeon, I. J. Byeon, G. Calero, J. Ahn, A. M. Gronenborn
Structural Basis Of Clade-Specific Engagement Of Samhd1 (Sterile Alpha Motif And Histidine/Aspartate-Containing Protein 1) Restriction Factors By Lentiviral Viral Protein (Vpx) Virulence Factors.
J. Biol. Chem. V. 290 17935 2015
PubMed-ID: 26045556  |  Reference-DOI: 10.1074/JBC.M115.665513

(-) Compounds

Molecule 1 - PROTEIN VPRBP
    Chains: A, D
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: BACULOVIRIDAE
    Expression System Strain: SF21
    Expression System Taxid: 10442
    Fragment: UNP RESIDUES 1057-1396
    Gene: VPRBP, DCAF1, KIAA0800, RIP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DDB1- AND CUL4-ASSOCIATED FACTOR 1,HIV-1 VPR-BINDING PROTEIN,VPRBP,SERINE/THREONINE-PROTEIN KINASE VPRBP,VPR-INTERACTING PROTEIN
 
Molecule 2 - VPX PROTEIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET43
    Expression System Strain: ROSETTA2 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VPX
    Organism Common: SIV
    Organism Scientific: SIMIAN IMMUNODEFICIENCY VIRUS
    Organism Taxid: 11723
 
Molecule 3 - SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41
    Expression System Strain: ROSETTA2 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL
    Gene: SAMHD1
    Organism Common: MANDRILL
    Organism Scientific: MANDRILLUS SPHINX
    Organism Taxid: 9561
    Synonym: SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:38 , HIS B:81 , CYS B:86binding site for residue ZN B 201
2AC2SOFTWAREHIS E:38 , HIS E:81 , CYS E:86binding site for residue ZN E 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z8L)

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Gln A:1158 -Pro A:1159
2Glu B:13 -Gly B:14
3Pro B:41 -Glu B:42
4Glu B:42 -Phe B:43
5Asp C:7 -Gln C:8
6Asp C:41 -Tyr C:42
7Gly C:60 -Glu C:61
8Gln D:1158 -Pro D:1159
9Glu E:13 -Gly E:14
10Pro E:41 -Glu E:42
11Glu E:42 -Phe E:43
12Asp F:7 -Gln F:8
13Arg F:20 -Thr F:21
14Asp F:41 -Tyr F:42
15Gly F:60 -Glu F:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z8L)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z8L)

(-) Sequences/Alignments

Asymmetric 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:305
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeeee.........eeeeee.....eeeeee...eeeeee.....eeeeee.......eeee.....eeeee.......eeeee.....eeeeee....eeee......eeeeee..eeeeee.....eeeee..............ee.....eeee..eeee....eeeee..........ee.....eeee..eeee.....eeee.hhhh.eeeee.....eeeeeee...eeeeeeeee.....eeeeee...eeeeeee.....eeeeeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z8l A 1073 RHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG 1390
                                  1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312 ||   1335      1345      1355      1365      1375      1385     
                                                                                                                                                                                                                                                                          1314|                                                              
                                                                                                                                                                                                                                                                           1328                                                              


Chain B from PDB  Type:PROTEIN  Length:79
                                                                                                                
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                4z8l B   10 EAPEGAGEVGLEQWLETSLERINREARLHFHPEFLFRLWNTCVEHWHDRHQRSLDYAKYRYLLLMHKAMYTHMQQGCPC   88
                                    19        29        39        49        59        69        79         


Chain C from PDB  Type:PROTEIN  Length:92
                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh.............hhhhhhhhhhhh...hhhhhh..........................hhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                4z8l C    2 QQADSDQPSKRPRFDDSPRGVELHPDYKTWGPEQVCFFLRRGGFGEPALLKNIRENKITGALLPCLDESHFENLGVSSLGERKKLLSYIQRS  107
                                    11        35        45        55        65        75        85        95       105  
                                             20|                                                                        
                                              35                                                                        


Chain D from PDB  Type:PROTEIN  Length:305
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeeee.........eeeeee.....eeeeee...eeeeee.....eeeeee.......eeee.....eeeee.......eeeee.....eeeeee....eeee......eeeeee..eeeeee.....eeeee..............ee.....eeee..eeee....eeeee..........ee.....eeee..eeee.....eeee.hhhh.eeeee.....eeeeeee...eeeeeeeee.....eeeeee...eeeeeee.....eeeeeee..........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z8l D 1073 RHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG 1390
                                  1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312 ||   1335      1345      1355      1365      1375      1385     
                                                                                                                                                                                                                                                                          1314|                                                              
                                                                                                                                                                                                                                                                           1328                                                              


Chain E from PDB  Type:PROTEIN  Length:79
                                                                                                                
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                4z8l E   10 EAPEGAGEVGLEQWLETSLERINREARLHFHPEFLFRLWNTCVEHWHDRHQRSLDYAKYRYLLLMHKAMYTHMQQGCPC   88
                                    19        29        39        49        59        69        79         


Chain F from PDB  Type:PROTEIN  Length:95
                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh..............hhhhhhhhhhhh......hhhhh.............hhhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                4z8l F    2 QQADSDQPSKRPRFDDSPRTGVELHPDYKTWGPEQVCFFLRRGGFGEPALLKNIRENKITGALLPCLDESHFENLGVSSLGERKKLLSYIQRSGQ  109
                                    11        21|       44        54        64        74        84        94       104     
                                              21|                                                                          
                                               35
   Legend:   → Mismatch (orange background)
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    → 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 4Z8L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z8L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z8L)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)

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  Q7ZB17_SIV | Q7ZB17
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCAF1_HUMAN | Q9Y4B6: 3wa0 4cc9 4p7i 4pxw 5aja 5jk7
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(-) Related Entries Specified in the PDB File

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