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- PDB-6zue: Crystal structure of human DDB1 bound to human DCAF1 (amino acid ... -

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Basic information

Entry
Database: PDB / ID: 6zue
TitleCrystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396)
Components
  • DDB1- and CUL4-associated factor 1
  • DNA damage-binding protein 1
KeywordsPROTEIN BINDING / Cullin-RING E3 ubiquitin ligase / Cullin 4 / ubiquitylation / DNA repair
Function / homology
Function and homology information


cell competition in a multicellular organism / histone H2AT120 kinase activity / V(D)J recombination / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding ...cell competition in a multicellular organism / histone H2AT120 kinase activity / V(D)J recombination / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-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 / viral release from host cell / ectopic germ cell programmed cell death / ubiquitin-like ligase-substrate adaptor activity / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / post-translational protein modification / B cell differentiation / nuclear estrogen receptor binding / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Wnt signaling pathway / fibrillar center / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein ubiquitination / protein serine kinase activity / DNA repair / apoptotic process / DNA damage response / centrosome / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller ...VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.094 Å
AuthorsSchwefel, D. / Taylor, I.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHW1851/1-1 Germany
CitationJournal: Plos Pathog. / Year: 2021
Title: Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses.
Authors: Banchenko, S. / Krupp, F. / Gotthold, C. / Burger, J. / Graziadei, A. / O'Reilly, F.J. / Sinn, L. / Ruda, O. / Rappsilber, J. / Spahn, C.M.T. / Mielke, T. / Taylor, I.A. / Schwefel, D.
History
DepositionJul 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: DDB1- and CUL4-associated factor 1


Theoretical massNumber of molelcules
Total (without water)169,7442
Polymers169,7442
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-15 kcal/mol
Surface area62250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.384, 153.626, 223.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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: 127241.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein kinase VPRBP / Vpr-interacting protein


Mass: 42502.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF1, KIAA0800, RIP, VPRBP / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100 mM Tri-Na citrate pH 5.5 18% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. obs: 36027 / % possible obs: 96.8 % / Redundancy: 4.82 % / CC1/2: 0.999 / Net I/σ(I): 12.98
Reflection shellResolution: 3.09→3.28 Å / Num. unique obs: 5769 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3e0c

3e0c


Resolution: 3.094→48.634 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 1780 4.96 %
Rwork0.222 34142 -
obs0.2249 35922 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 274.9 Å2 / Biso mean: 113.7834 Å2 / Biso min: 45.66 Å2
Refinement stepCycle: final / Resolution: 3.094→48.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11269 0 0 10 11279
Biso mean---71.7 -
Num. residues----1428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411498
X-RAY DIFFRACTIONf_angle_d0.75915568
X-RAY DIFFRACTIONf_chiral_restr0.051777
X-RAY DIFFRACTIONf_plane_restr0.0052006
X-RAY DIFFRACTIONf_dihedral_angle_d6.0449582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.094-3.17750.41071320.3676253294
3.1775-3.2710.43471460.3591266998
3.271-3.37660.35731360.353260598
3.3766-3.49720.39961460.3124261198
3.4972-3.63720.35841370.2953263498
3.6372-3.80270.37011470.2802261697
3.8027-4.0030.30491390.2527263198
4.003-4.25370.29561260.2254265198
4.2537-4.58190.26421270.1875264497
4.5819-5.04260.22151390.1728261596
5.0426-5.77120.24511440.1901262696
5.7712-7.26730.26011250.2123263295
7.2673-48.6340.23291360.1807267693
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)
10.6045-0.61610.31241.0581-0.42330.60.01740.0162-0.07310.0322-0.05250.07450.1473-0.110400.738-0.0240.09850.8049-0.10240.81157.181932.37422.2085
21.0450.4547-0.12470.87030.19430.8478-0.01480.19120.0211-0.15780.1430.0170.2783-0.1483-01.0325-0.0125-0.04030.92270.0260.733737.7245-9.808924.2035
30.6791-0.231-0.84011.69410.19811.7588-0.10630.0368-0.01670.39160.0776-0.2830.2985-0.0392-0.22050.65420.113-0.11530.6468-0.00260.675924.903433.622346.7113
40.3961-0.328-0.18780.4218-0.05720.3569-0.33830.27470.14720.19610.3286-0.37940.0399-0.1614-0.00170.90390.0825-0.28730.9052-0.02031.071427.265465.183645.5404
50.0278-0.0073-0.03740.0314-0.07090.04050.03160.34630.09680.1814-0.729-0.0579-0.43880.11830.00040.924-0.1402-0.13450.87550.10811.613737.525778.252633.0173
60.1834-0.062-0.04820.0127-0.02410.2463-0.54840.23580.4867-0.44690.18840.2837-0.33050.19840.00020.93890.0217-0.09030.85430.10841.089522.027479.604522.6883
7-0.03160.381-0.22580.8617-0.26020.2675-0.14210.01840.08980.20190.0131-0.1254-0.61460.0060.00010.9560.148-0.14390.9534-0.02550.874315.347567.97541.3145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 413 )A1 - 413
2X-RAY DIFFRACTION2chain 'A' and (resid 414 through 709 )A414 - 709
3X-RAY DIFFRACTION3chain 'A' and (resid 710 through 1140 )A710 - 1140
4X-RAY DIFFRACTION4chain 'B' and (resid 1046 through 1143 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1144 through 1171 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1172 through 1264 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1265 through 1400 )B0

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