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- PDB-3ei1: Structure of hsDDB1-drDDB2 bound to a 14 bp 6-4 photoproduct cont... -

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Basic information

Entry
Database: PDB / ID: 3ei1
TitleStructure of hsDDB1-drDDB2 bound to a 14 bp 6-4 photoproduct containing DNA-duplex
Components
  • (DNA damage-binding protein ...) x 2
  • 5'-D(*DAP*DCP*DGP*DCP*DGP*DAP*(64T)P*(5PY)P*DGP*DCP*DGP*DCP*DCP*DC)-3'
  • 5'-D(*DTP*DGP*DGP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DGP*DCP*DG)-3'
KeywordsDNA BINDING PROTEIN/DNA / UV-damage / DDB / nucleotide excision repair / xeroderma pigmentosum / Alternative splicing / Disease mutation / DNA damage / DNA repair / DNA-binding / Nucleus / Phosphoprotein / Polymorphism / WD repeat / Ubl conjugation pathway / DNA BINDING PROTEIN-DNA COMPLEX
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 / 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 / site of DNA damage / cullin family protein binding / 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 / 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 / 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 / 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
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 / DNA (> 10) / 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: 2.8 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 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
G: 5'-D(*DAP*DCP*DGP*DCP*DGP*DAP*(64T)P*(5PY)P*DGP*DCP*DGP*DCP*DCP*DC)-3'
H: 5'-D(*DTP*DGP*DGP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DGP*DCP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,5735
Polymers181,3794
Non-polymers1941
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-30 kcal/mol
Surface area63350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.740, 123.600, 158.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA damage-binding protein ... , 2 types, 2 molecules AB

#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 / Damage-specific DNA-binding protein 2


Mass: 43559.113 Da / Num. of mol.: 1
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

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DNA chain , 2 types, 2 molecules GH

#3: DNA chain 5'-D(*DAP*DCP*DGP*DCP*DGP*DAP*(64T)P*(5PY)P*DGP*DCP*DGP*DCP*DCP*DC)-3'


Mass: 4243.772 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 5'-D(*DTP*DGP*DGP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DGP*DCP*DG)-3'


Mass: 4321.803 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 2 types, 194 molecules

#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.04 Å3/Da / Density % sol: 59.56 %
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
Components of the solutions
IDNameCrystal-IDSol-ID
1Ca-Acetate11
2MES11
3PEG 40011
4Ca-Acetate12
5MES12
6PEG 40012

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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: 2.8→97.59 Å / Num. all: 56150 / Num. obs: 56150 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 50.272 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 23.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 39873 / Num. unique all: 5526 / Num. unique obs: 5526 / Rsym value: 0.44 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementResolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 0 / SU B: 14.574 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.65 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2724 5.1 %RANDOM
Rwork0.22 ---
obs0.223 53750 97.41 %-
all-53750 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.49 Å2 / Biso mean: 44.567 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2---1.67 Å20 Å2
3---2.9 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11552 568 13 193 12326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212414
X-RAY DIFFRACTIONr_angle_refined_deg1.1582.01916948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26551463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11324.48538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.442152045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2551566
X-RAY DIFFRACTIONr_chiral_restr0.0760.21926
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219139
X-RAY DIFFRACTIONr_mcbond_it0.4751.57279
X-RAY DIFFRACTIONr_mcangle_it0.875211795
X-RAY DIFFRACTIONr_scbond_it0.77535135
X-RAY DIFFRACTIONr_scangle_it1.3964.55153
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 205 -
Rwork0.299 3633 -
all-3838 -
obs--95 %

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