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- PDB-5jk7: The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex -

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Basic information

Entry
Database: PDB / ID: 5jk7
TitleThe X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex
Components
  • DNA damage-binding protein 1
  • Protein VPRBP
  • Protein Vpr
  • Uracil-DNA glycosylase
KeywordsViral protein/DNA BINDING PROTEIN / Cullin4-RING E3 ubiquitin ligase HIV-1 Vpr UNG2 / DNA BINDING PROTEIN-HYDROLASE complex / Viral protein-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


histone H2AT120 kinase activity / cell competition in a multicellular organism / symbiont-mediated arrest of host cell cycle during G2/M transition / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / positive regulation by virus of viral protein levels in host cell / V(D)J recombination / isotype switching ...histone H2AT120 kinase activity / cell competition in a multicellular organism / symbiont-mediated arrest of host cell cycle during G2/M transition / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / positive regulation by virus of viral protein levels in host cell / V(D)J recombination / isotype switching / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / uracil DNA N-glycosylase activity / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / ribosomal small subunit binding / ubiquitin-like ligase-substrate adaptor activity / viral release from host cell / somatic hypermutation of immunoglobulin genes / ectopic germ cell programmed cell death / positive regulation of viral genome replication / positive regulation of gluconeogenesis / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / monoatomic ion transmembrane transport / post-translational protein modification / B cell differentiation / Chromatin modifications during the maternal to zygotic transition (MZT) / virion component / nuclear estrogen receptor binding / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / DNA Damage Recognition in GG-NER / base-excision repair / : / protein homooligomerization / Dual Incision in GG-NER / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / viral penetration into host nucleus / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / host extracellular space / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / non-specific serine/threonine protein kinase / cell cycle / symbiont entry into host cell / phosphorylation / DNA repair / protein serine kinase activity / DNA-templated transcription / apoptotic process / DNA damage response / host cell nucleus / protein-containing complex binding / nucleolus / regulation of DNA-templated transcription / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / 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 / DNA polymerase; domain 1 - #910 / Uracil-DNA glycosylase family 1 / Lissencephaly type-1-like homology motif / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4730 / Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / DNA polymerase; domain 1 - #910 / Uracil-DNA glycosylase family 1 / Lissencephaly type-1-like homology motif / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Uracil-DNA glycosylase-like domain superfamily / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / DNA polymerase; domain 1 / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein Vpr / Uracil-DNA glycosylase / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.49 Å
AuthorsCalero, G. / Ahn, J. / Wu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM082251 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction.
Authors: Wu, Y. / Zhou, X. / Barnes, C.O. / DeLucia, M. / Cohen, A.E. / Gronenborn, A.M. / Ahn, J. / Calero, G.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: DNA damage-binding protein 1
B: DNA damage-binding protein 1
C: Protein VPRBP
D: Uracil-DNA glycosylase
E: Protein VPRBP
F: Protein Vpr
G: Uracil-DNA glycosylase
H: Protein Vpr


Theoretical massNumber of molelcules
Total (without water)410,1118
Polymers410,1118
Non-polymers00
Water0
1
A: DNA damage-binding protein 1
C: Protein VPRBP
G: Uracil-DNA glycosylase
H: Protein Vpr


Theoretical massNumber of molelcules
Total (without water)205,0564
Polymers205,0564
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA damage-binding protein 1
D: Uracil-DNA glycosylase
E: Protein VPRBP
F: Protein Vpr


Theoretical massNumber of molelcules
Total (without water)205,0564
Polymers205,0564
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.900, 128.200, 129.200
Angle α, β, γ (deg.)75.11, 89.44, 65.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q16531
#2: 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: 41178.234 Da / Num. of mol.: 2 / Fragment: UNP residues 1045-1396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPRBP, DCAF1, KIAA0800, RIP
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#3: Protein Uracil-DNA glycosylase / / UDG


Mass: 25382.957 Da / Num. of mol.: 2 / Fragment: UNP residues 85-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNG, DGU, UNG1, UNG15
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P13051, uracil-DNA glycosylase
#4: Protein Protein Vpr / R ORF protein / Viral protein R


Mass: 11396.878 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Strain: isolate NY5 / Gene: vpr
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P12520

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.91 %
Crystal growTemperature: 289.15 K / Method: batch mode / Details: 100 mM Na Ctrate, pH 5.6, 11% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.49→40.3 Å / Num. obs: 77315 / Biso Wilson estimate: 188.78 Å2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 3.49→40.3 Å / Cor.coef. Fo:Fc: 0.9415 / Cor.coef. Fo:Fc free: 0.9297 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.422
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 2463 3.19 %RANDOM
Rwork0.1761 ---
obs0.1771 77315 90.57 %-
Displacement parametersBiso mean: 193.89 Å2
Baniso -1Baniso -2Baniso -3
1-35.4144 Å28.5994 Å2-3.5484 Å2
2---12.8258 Å230.1584 Å2
3----22.5886 Å2
Refine analyzeLuzzati coordinate error obs: 1.036 Å
Refinement stepCycle: LAST / Resolution: 3.49→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27701 0 0 0 27701
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0128308HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3438379HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9774SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes732HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4086HARMONIC5
X-RAY DIFFRACTIONt_it28308HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion23.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3683SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact32509SEMIHARMONIC4
LS refinement shellResolution: 3.49→3.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2822 37 3.78 %
Rwork0.2615 943 -
all0.2622 980 -
obs--90.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8735-0.233-0.33951.396-0.11340.6524-0.1507-0.4977-0.2269-0.07080.3810.38240.0901-0.4685-0.2303-0.5573-0.1195-0.2236-0.04210.2540.1232-17.5742-14.4232-0.5646
23.4853-1.29411.43784.12351.17734.92640.02051.04920.2361-1.2996-0.1968-1.32-0.15981.5590.17630.55610.37740.30360.3836-0.0566-0.325568.702110.2577-70.1731
34.62570.3461.13062.7789-0.86892.2006-0.06930.0773-1.0783-0.11310.0697-0.2603-0.10750.2414-0.0004-0.4281-0.0610.0884-0.1917-0.24830.316230.4255-4.3545-4.6433
44.727-2.4286-0.83115.8435-0.18792.86340.0341-0.41580.43220.47940.04810.3427-0.8711-0.2353-0.08210.42320.11630.1082-0.4209-0.4008-0.170216.600743.17057.0215
52.5289-1.9194-0.43833.66670.67294.68810.32350.6231-0.2358-0.2561-0.33940.3317-0.3277-0.4570.0160.01160.0237-0.1727-0.3157-0.1579-0.30730.348827.4504-43.9669
64.84480.4179-3.32942.2099-0.15567.2293-0.07210.37330.045-0.40960.10240.5177-0.1924-0.4981-0.03030.03420.1401-0.0019-0.5551-0.08950.022722.051737.7883-20.5679
76.7360.28451.70483.9903-1.07823.7730.048-0.29170.25660.059-0.2285-0.5395-0.57160.71020.1805-0.0825-0.5146-0.1421-0.1041-0.09980.133665.090837.9829-8.1119
87.61763.76-3.63453.5234-2.67755.96020.0094-0.0646-0.23250.144-0.104-0.13410.10820.33450.0946-0.5701-0.1261-0.1154-0.2785-0.1341-0.23949.286614.6677-4.0451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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