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- PDB-6fcv: Structure of the human DDB1-CSA complex -

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Basic information

Entry
Database: PDB / ID: 6fcv
TitleStructure of the human DDB1-CSA complex
Components
  • DNA damage-binding protein 1
  • DNA excision repair protein ERCC-8
KeywordsPROTEIN BINDING / DNA DAMAGE RESPONSE PROTEIN
Function / homology
Function and homology information


regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / double-strand break repair via classical nonhomologous end joining / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont ...regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / double-strand break repair via classical nonhomologous end joining / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / 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 / response to X-ray / viral release from host cell / transcription-coupled nucleotide-excision repair / ectopic germ cell programmed cell death / protein autoubiquitination / positive regulation of viral genome replication / response to UV / positive regulation of gluconeogenesis / positive regulation of DNA repair / proteasomal protein catabolic process / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / nuclear matrix / protein polyubiquitination / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / rhythmic process / cellular response to UV / protein-macromolecule adaptor activity / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / response to oxidative stress / chromosome, telomeric region / damaged DNA binding / 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
DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / 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 ...DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA excision repair protein ERCC-8 / DNA damage-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsMeulenbroek, E.M. / Pannu, N.S.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
NWOTOP Talent-021.002.024 Netherlands
NWOVIDI-700.55.425 Netherlands
CitationJournal: Nat Commun / Year: 2018
Title: TRiC controls transcription resumption after UV damage by regulating Cockayne syndrome protein A.
Authors: Pines, A. / Dijk, M. / Makowski, M. / Meulenbroek, E.M. / Vrouwe, M.G. / van der Weegen, Y. / Baltissen, M. / French, P.J. / van Royen, M.E. / Luijsterburg, M.S. / Mullenders, L.H. / ...Authors: Pines, A. / Dijk, M. / Makowski, M. / Meulenbroek, E.M. / Vrouwe, M.G. / van der Weegen, Y. / Baltissen, M. / French, P.J. / van Royen, M.E. / Luijsterburg, M.S. / Mullenders, L.H. / Vermeulen, M. / Vermeulen, W. / Pannu, N.S. / van Attikum, H.
History
DepositionDec 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.2Jan 17, 2024Group: 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 excision repair protein ERCC-8


Theoretical massNumber of molelcules
Total (without water)175,6962
Polymers175,6962
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-13 kcal/mol
Surface area59640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.790, 140.790, 249.331
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 129253.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein DNA excision repair protein ERCC-8 / Cockayne syndrome WD repeat protein CSA


Mass: 46441.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC8, CKN1, CSA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13216

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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: 4.06 Å3/Da / Density % sol: 69.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate, 24% PEG 3350, 0.1 M bis-tris propane pH 8.0, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→87.17 Å / Num. obs: 55130 / % possible obs: 89.5 % / Redundancy: 3.96 % / Rpim(I) all: 0.059 / Net I/σ(I): 6.8
Reflection shellResolution: 2.9→3.06 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8564 / Rpim(I) all: 0.43 / % possible all: 92.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A11

4a11


Resolution: 2.92→68.67 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.792 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24528 2867 5.1 %RANDOM
Rwork0.19296 ---
obs0.19557 52821 88.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.441 Å2
Baniso -1Baniso -2Baniso -3
1-34.83 Å20 Å20 Å2
2--34.83 Å20 Å2
3----69.65 Å2
Refinement stepCycle: 1 / Resolution: 2.92→68.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11412 0 0 0 11412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911625
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210776
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.9615741
X-RAY DIFFRACTIONr_angle_other_deg0.72325020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24851447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29324.381525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.728152038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4461568
X-RAY DIFFRACTIONr_chiral_restr0.0670.21805
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212877
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022311
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.6728.8875815
X-RAY DIFFRACTIONr_mcbond_other7.6658.8865814
X-RAY DIFFRACTIONr_mcangle_it11.26913.3077253
X-RAY DIFFRACTIONr_mcangle_other11.26813.3087254
X-RAY DIFFRACTIONr_scbond_it7.3389.2165810
X-RAY DIFFRACTIONr_scbond_other7.3379.2165811
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.65513.6778489
X-RAY DIFFRACTIONr_long_range_B_refined1747458
X-RAY DIFFRACTIONr_long_range_B_other16.99947459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.92→2.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 240 -
Rwork0.278 3978 -
obs--91.82 %

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