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- PDB-3ei3: Structure of the hsDDB1-drDDB2 complex -

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Basic information

Entry
Database: PDB / ID: 3ei3
TitleStructure of the hsDDB1-drDDB2 complex
Components
  • DNA damage-binding protein 1
  • DNA damage-binding protein 2
KeywordsDNA BINDING PROTEIN / UV-damage / DDB / nucleotide excision repair / xeroderma pigmentosum / Cytoplasm / DNA damage / DNA repair / DNA-binding / Host-virus interaction / Nucleus / Phosphoprotein / Polymorphism / Ubl conjugation pathway / WD repeat
Function / homology
Function and homology information


DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Neddylation / Ub-specific processing proteases / 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 ...DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Neddylation / Ub-specific processing proteases / 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 / 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 / site of DNA damage / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / response to UV / positive regulation of gluconeogenesis / 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 / 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 / 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
Helix Hairpins - #3280 / DNA damage-binding protein 2 / 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 ...Helix Hairpins - #3280 / DNA damage-binding protein 2 / 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 / Helix Hairpins / 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 damage-binding protein 1 / DNA damage-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsScrima, A. / Thoma, N.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex.
Authors: Scrima, A. / Konickova, R. / Czyzewski, B.K. / Kawasaki, Y. / Jeffrey, P.D. / Groisman, R. / Nakatani, Y. / Iwai, S. / Pavletich, N.P. / Thoma, N.H.
History
DepositionSep 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2019Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell / Item: _reflns_shell.pdbx_Rsym_value
Revision 1.3Mar 20, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,0073
Polymers172,8132
Non-polymers1941
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-16 kcal/mol
Surface area60300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.440, 114.360, 173.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA damage-binding protein 1 / hsDDB1 / Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 subunit / ...hsDDB1 / Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 subunit / DNA damage-binding protein a / DDBa / UV-damaged DNA-binding protein 1 / UV-DDB 1 / Xeroderma pigmentosum group E-complementing protein / XPCe / XPE-binding factor / XPE-BF / HBV X-associated protein 1 / XAP-1


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 / Cell (production host): high five cells / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531
#2: Protein DNA damage-binding protein 2 / drDDB2 / 'Damage-specific DNA-binding protein 2


Mass: 43559.113 Da / Num. of mol.: 1 / Fragment: residues 75-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ddb2, si:dkey-45f10.3 / Cell (production host): high five cells / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2YDS1
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 100mM Ca-Acetate, 100mM MES pH 5.7, 12-14% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 2.3→95.35 Å / Num. all: 96994 / Num. obs: 96994 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 40.476 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.7 / Num. measured obs: 70873 / Num. unique all: 11488 / Num. unique obs: 11488 / Rsym value: 0.406 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementResolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0 / SU B: 6.306 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4861 5 %RANDOM
Rwork0.208 ---
obs0.21 96993 99.77 %-
all-96993 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.4 Å2 / Biso mean: 36.868 Å2 / Biso min: 12.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---2.26 Å20 Å2
3---3.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11536 0 13 697 12246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211739
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.95815920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49751461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17624.615533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.814152025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5041560
X-RAY DIFFRACTIONr_chiral_restr0.0810.21813
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218816
X-RAY DIFFRACTIONr_mcbond_it0.6191.57268
X-RAY DIFFRACTIONr_mcangle_it1.156211772
X-RAY DIFFRACTIONr_scbond_it1.28434471
X-RAY DIFFRACTIONr_scangle_it2.2244.54147
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 328 -
Rwork0.242 6757 -
all-7085 -
obs--99.72 %

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