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- PDB-4z8l: Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex -

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Basic information

Entry
Database: PDB / ID: 4z8l
TitleCrystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex
Components
  • Protein VPRBP
  • SAM domain and HD domain-containing protein
  • Vpx protein
KeywordsViral Protein/VPX-BINDING PROTEIN / HIV / antiviral defense / Viral Protein-VPX-BINDING PROTEIN complex
Function / homology
Function and homology information


cell competition in a multicellular organism / dGTPase activity / dGTP catabolic process / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / regulation of innate immune response / ubiquitin-like ligase-substrate adaptor activity / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding ...cell competition in a multicellular organism / dGTPase activity / dGTP catabolic process / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / regulation of innate immune response / ubiquitin-like ligase-substrate adaptor activity / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / virion component / fibrillar center / viral penetration into host nucleus / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / host cell / chromosome / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / DNA replication / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein ubiquitination / symbiont entry into host cell / protein serine kinase activity / DNA repair / centrosome / host cell nucleus / GTP binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4730 / Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / : / LIS1 homology (LisH) motif profile. / LIS1 homology motif / HD domain profile. ...: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4730 / Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / : / LIS1 homology (LisH) motif profile. / LIS1 homology motif / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / Protein Vpr / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Simian immunodeficiency virus
Mandrillus sphinx (mandrill)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKoharudin, L.M. / Wu, Y. / Calero, G. / Ahn, J. / Gronenborn, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM82251 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis of Clade-specific Engagement of SAMHD1 (Sterile alpha Motif and Histidine/Aspartate-containing Protein 1) Restriction Factors by Lentiviral Viral Protein X (Vpx) Virulence Factors.
Authors: Wu, Y. / Koharudin, L.M. / Mehrens, J. / DeLucia, M. / Byeon, C.H. / Byeon, I.J. / Calero, G. / Ahn, J. / Gronenborn, A.M.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein VPRBP
B: Vpx protein
C: SAM domain and HD domain-containing protein
D: Protein VPRBP
E: Vpx protein
F: SAM domain and HD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,4918
Polymers130,3606
Non-polymers1312
Water2,054114
1
A: Protein VPRBP
B: Vpx protein
C: SAM domain and HD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2464
Polymers65,1803
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-62 kcal/mol
Surface area21610 Å2
MethodPISA
2
D: Protein VPRBP
E: Vpx protein
F: SAM domain and HD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2464
Polymers65,1803
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-60 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.490, 74.490, 178.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Protein VPRBP / DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein ...DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein kinase VPRBP / Vpr-interacting protein


Mass: 39777.664 Da / Num. of mol.: 2 / Fragment: UNP residues 1057-1396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPRBP, DCAF1, KIAA0800, RIP / Production host: Baculoviridae (virus) / Strain (production host): SF21
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#2: Protein Vpx protein


Mass: 12204.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Gene: vpx / Plasmid: pET43 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 / References: UniProt: Q7ZB17
#3: Protein SAM domain and HD domain-containing protein / SAM domain and HD domain-containing protein 1


Mass: 13197.734 Da / Num. of mol.: 2 / Fragment: N-terminal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mandrillus sphinx (mandrill) / Gene: SAMHD1 / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 / References: UniProt: H6WEA4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2014
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→43.7 Å / Num. obs: 33447 / % possible obs: 98.29 % / Redundancy: 9.1 % / Net I/σ(I): 12.7
Reflection shellResolution: 2.6→2.72 Å / % possible obs: 89.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 1.818 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.383 / Rpim(I) all: 0.782

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
d*TREKdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CC9, 2E8O

4cc9

2e8o


Resolution: 2.6→43.695 Å / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 25.96 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 1005 3 %Random selection
Rwork0.1992 ---
obs0.2015 33447 98.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→43.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7712 0 2 114 7828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077902
X-RAY DIFFRACTIONf_angle_d1.42810685
X-RAY DIFFRACTIONf_dihedral_angle_d15.8552883
X-RAY DIFFRACTIONf_chiral_restr0.0611137
X-RAY DIFFRACTIONf_plane_restr0.0071394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6005-2.73760.39541320.31644249X-RAY DIFFRACTION87
2.7376-2.90910.3211430.23824628X-RAY DIFFRACTION97
2.9091-3.13370.27661480.21514773X-RAY DIFFRACTION97
3.1337-3.44890.24661440.20564680X-RAY DIFFRACTION97
3.4489-3.94770.26121450.20854687X-RAY DIFFRACTION96
3.9477-4.97250.1691470.15634727X-RAY DIFFRACTION97
4.9725-43.70070.17111450.19254687X-RAY DIFFRACTION97

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