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- PDB-6dsz: Crystal structure of DDB1 in complex with DET1- and DDB1-associat... -

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Basic information

Entry
Database: PDB / ID: 6dsz
TitleCrystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1)
Components
  • DET1- and DDB1-associated protein 1
  • DNA damage-binding protein 1
KeywordsLIGASE / E3 Ubiquitin Ligase Cul4 RING Ligases CRL4 DDB1(DNA damage-binding protein 1) DDA1(DDB1 and DET1 associated 1)
Function / homology
Function and homology information


positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / 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 / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / 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 / 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 / positive regulation of viral genome replication / positive regulation of gluconeogenesis / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / protein polyubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / DNA polymerase; domain 1 - #910 / 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 ...DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / DNA polymerase; domain 1 - #910 / 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 / DNA polymerase; domain 1 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA damage-binding protein 1 / DET1- and DDB1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.093 Å
AuthorsShabek, N. / Zheng, N.
CitationJournal: Cell Discov / Year: 2018
Title: Structural insights into DDA1 function as a core component of the CRL4-DDB1 ubiquitin ligase.
Authors: Shabek, N. / Ruble, J. / Waston, C.J. / Garbutt, K.C. / Hinds, T.R. / Li, T. / Zheng, N.
History
DepositionJun 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: DNA damage-binding protein 1
C: DET1- and DDB1-associated protein 1
D: DET1- and DDB1-associated protein 1


Theoretical massNumber of molelcules
Total (without water)258,6704
Polymers258,6704
Non-polymers00
Water0
1
A: DNA damage-binding protein 1
C: DET1- and DDB1-associated protein 1


Theoretical massNumber of molelcules
Total (without water)129,3352
Polymers129,3352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-12 kcal/mol
Surface area48250 Å2
MethodPISA
2
B: DNA damage-binding protein 1
D: DET1- and DDB1-associated protein 1


Theoretical massNumber of molelcules
Total (without water)129,3352
Polymers129,3352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-12 kcal/mol
Surface area47470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.196, 219.175, 89.317
Angle α, β, γ (deg.)90.000, 89.980, 90.000
Int Tables number4
Space group name H-MP1211

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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: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531
#2: Protein/peptide DET1- and DDB1-associated protein 1 / Placenta cross-immune reaction antigen 1 / PCIA-1


Mass: 2237.599 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BW61

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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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES monohydrate, pH 6.5, 20% (w/v) PEG4000, 180 mM NaCl, 5 mM DTT

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Data collection

DiffractionMean temperature: 155 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.093→47.8 Å / Num. obs: 40025 / % possible obs: 89 % / Redundancy: 2.7 % / CC1/2: 0.99 / Rpim(I) all: 0.064 / Rrim(I) all: 0.151 / Net I/σ(I): 10.29
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2.7 % / Num. unique obs: 2174 / CC1/2: 0.746 / Rpim(I) all: 0.373 / Rrim(I) all: 0.151

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B5M

2b5m


Resolution: 3.093→47.796 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.11
RfactorNum. reflection% reflection
Rfree0.3071 1997 5.09 %
Rwork0.247 --
obs0.2501 39216 88.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 191.24 Å2 / Biso mean: 55.135 Å2 / Biso min: 4.95 Å2
Refinement stepCycle: final / Resolution: 3.093→47.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17408 0 0 0 17408
Num. residues----2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417717
X-RAY DIFFRACTIONf_angle_d0.77323965
X-RAY DIFFRACTIONf_chiral_restr0.0492767
X-RAY DIFFRACTIONf_plane_restr0.0043071
X-RAY DIFFRACTIONf_dihedral_angle_d15.86610673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0932-3.17060.3321710.31521400147147
3.1706-3.25630.3486950.30511729182459
3.2563-3.35210.36741090.27942145225471
3.3521-3.46020.35571190.28522383250280
3.4602-3.58380.40261420.28782687282989
3.5838-3.72730.34531630.27812921308496
3.7273-3.89690.41151590.266129703129100
3.8969-4.10220.33571650.252329603125100
4.1022-4.3590.31791600.234629773137100
4.359-4.69530.22071650.205130293194100
4.6953-5.16740.291590.206630093168100
5.1674-5.91390.28081590.243929873146100
5.9139-7.44630.30021660.253730263192100
7.4463-47.80140.25111650.23222996316199

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