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- PDB-4a11: Structure of the hsDDB1-hsCSA complex -

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Basic information

Entry
Database: PDB / ID: 4a11
TitleStructure of the hsDDB1-hsCSA complex
Components
  • DNA DAMAGE-BINDING PROTEIN 1
  • DNA EXCISION REPAIR PROTEIN ERCC-8
KeywordsDNA BINDING PROTEIN / DNA DAMAGE REPAIR
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 / double-strand break repair via classical nonhomologous end joining / 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 transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / double-strand break repair via classical nonhomologous end joining / 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 / response to X-ray / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / transcription-coupled nucleotide-excision repair / response to UV / protein autoubiquitination / positive regulation of gluconeogenesis / positive regulation of DNA repair / 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 / Wnt signaling pathway / Formation of Incision Complex in GG-NER / nuclear matrix / Dual incision in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / response to oxidative stress / 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 / negative regulation of apoptotic process / nucleolus / 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 / 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 ...DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / DNA polymerase; domain 1 - #910 / 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 / DNA polymerase; domain 1 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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: 3.31 Å
AuthorsBohm, K. / Scrima, A. / Fischer, E.S. / Gut, H. / Thomae, N.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation.
Authors: Fischer, E.S. / Scrima, A. / Bohm, K. / Matsumoto, S. / Lingaraju, G.M. / Faty, M. / Yasuda, T. / Cavadini, S. / Wakasugi, M. / Hanaoka, F. / Iwai, S. / Gut, H. / Sugasawa, K. / Thoma, N.H.
History
DepositionSep 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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 EXCISION REPAIR PROTEIN ERCC-8


Theoretical massNumber of molelcules
Total (without water)174,8612
Polymers174,8612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-17.2 kcal/mol
Surface area55230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.330, 138.330, 244.970
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 / COCKAYNE SYNDROME A PROTEIN


Mass: 129394.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC-DERIVED / Cell line (production host): High Five / Production host: TRICHOPULSIA NI (cabbage looper) / References: UniProt: Q16531
#2: Protein DNA EXCISION REPAIR PROTEIN ERCC-8 / COCKAYNE SYNDROME WD REPEAT PROTEIN CSA / UV-DAMAGED DNA-BINDING PROTEIN 1


Mass: 45465.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC-DERIVED / Cell line (production host): High Five / Production host: TRICHOPULSIA NI (cabbage looper) / References: UniProt: Q13216

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 8
Details: 1.4-1.58 M NAKPO4, 0.1 M NAMALONATE, 0-0.1 M LI2SO4, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 38124 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 80.81 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.03
Reflection shellResolution: 3.31→3.39 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.95 / % possible all: 78.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EI3

3ei3


Resolution: 3.31→32.067 Å / SU ML: 0.69 / σ(F): 1.99 / Phase error: 21.77 / Stereochemistry target values: ML
Details: UNMODELLED DENSITY WAS OBSERVED CLOSE THE THE DDB1-BPB DOMAIN POTENTIALLY REFLECTING A MAINLY UNSTRUCTURED LOOP REGION OF DDB1.
RfactorNum. reflection% reflection
Rfree0.2331 1908 5 %
Rwork0.1757 --
obs0.1785 38079 92.67 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.497 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 84.02 Å2
Baniso -1Baniso -2Baniso -3
1-13.1042 Å20 Å20 Å2
2--13.1042 Å20 Å2
3----26.2084 Å2
Refinement stepCycle: LAST / Resolution: 3.31→32.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11081 0 0 0 11081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911294
X-RAY DIFFRACTIONf_angle_d1.34215366
X-RAY DIFFRACTIONf_dihedral_angle_d16.1163988
X-RAY DIFFRACTIONf_chiral_restr0.0871805
X-RAY DIFFRACTIONf_plane_restr0.0061977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3105-3.39320.30671130.25072238X-RAY DIFFRACTION81
3.3932-3.48480.31891250.24662546X-RAY DIFFRACTION93
3.4848-3.58720.27851530.2322573X-RAY DIFFRACTION94
3.5872-3.70290.24851350.2112605X-RAY DIFFRACTION94
3.7029-3.8350.26871520.19942602X-RAY DIFFRACTION95
3.835-3.98830.26771420.18772582X-RAY DIFFRACTION94
3.9883-4.16940.19721480.15972564X-RAY DIFFRACTION93
4.1694-4.38870.23281070.14252645X-RAY DIFFRACTION95
4.3887-4.66290.20181490.13262602X-RAY DIFFRACTION94
4.6629-5.02170.18811290.13612639X-RAY DIFFRACTION94
5.0217-5.52470.22241210.14612635X-RAY DIFFRACTION93
5.5247-6.31890.22491540.16452634X-RAY DIFFRACTION94
6.3189-7.94110.20331370.16852671X-RAY DIFFRACTION94
7.9411-32.06840.24071430.20332635X-RAY DIFFRACTION89

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