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- PDB-9ejq: Crystal structure of DDB1 in complex with XS381952 -

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Basic information

Entry
Database: PDB / ID: 9ejq
TitleCrystal structure of DDB1 in complex with XS381952
ComponentsDNA damage-binding protein 1
KeywordsLIGASE / WD-repeat / WDR / DDB1 / E3-ligase / ligand / SGC
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 / proteasomal protein catabolic process / positive regulation of gluconeogenesis / 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 / Dual incision in TC-NER / 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 / 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
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 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / L(+)-TARTARIC ACID / DNA damage-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.87 Å
AuthorsZeng, H. / Ahmad, H. / Wang, X. / Sun, J. / Dong, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Peng, H. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of DDB1 in complex with XS381952
Authors: Zeng, H. / Ahmad, H. / Wang, X. / Sun, J. / Dong, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Peng, H. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionNov 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,48127
Polymers127,2561
Non-polymers2,22526
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.640, 124.700, 167.716
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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Protein , 1 types, 1 molecules A

#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: 127255.625 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

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Non-polymers , 7 types, 644 molecules

#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-A1BIX / (4S)-4-(3-ethoxyphenyl)-3-methyl-1-[(4R)-[1,2,4]triazolo[4,3-b]pyridazin-6-yl]-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-b]pyridin-6-one


Mass: 389.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N7O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20.0 P3350, 0.2 di-NH4tart

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 99776 / % possible obs: 91.2 % / Redundancy: 4.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.034 / Rrim(I) all: 0.077 / Χ2: 1.307 / Net I/σ(I): 13.1 / Num. measured all: 429746
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.87-1.94.70.9450930.6660.8940.461.0511.25294.1
1.9-1.944.70.76150060.7140.9130.3750.8521.27192.7
1.94-1.974.60.59549420.7950.9410.2960.6671.31991.6
1.97-2.014.50.49549150.820.9490.2480.5561.36290.2
2.01-2.064.50.40847950.870.9650.2060.4591.37989.2
2.06-2.114.40.34947900.9060.9750.1760.3931.39288.3
2.11-2.164.30.29847640.930.9820.1510.3361.4487.3
2.16-2.224.20.24346640.9430.9850.1250.2751.41486.5
2.22-2.2840.2246240.9560.9890.1140.2491.43285.6
2.28-2.3640.18945780.9640.9910.0980.2151.4283.8
2.36-2.443.90.17145420.9670.9920.090.1951.46783.8
2.44-2.543.70.15146270.9740.9930.080.1721.44385
2.54-2.653.60.12447710.9830.9960.0670.1421.49187.3
2.65-2.793.50.09650340.9880.9970.0530.1111.40191.9
2.79-2.973.60.07452220.990.9970.0420.0861.29895.5
2.97-3.23.80.05753840.9950.9990.0320.0661.15898.2
3.2-3.524.20.04754810.9550.9880.0250.0541.21599.3
3.52-4.034.90.04155520.9980.9990.020.0461.31799.9
4.03-5.075.20.03455550.99910.0160.0381.13399.3
5.07-505.60.03354370.99910.0150.0370.97192.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.87→25.1 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.841 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22024 4984 5 %RANDOM
Rwork0.16107 ---
obs0.16396 94637 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.997 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å2-0 Å20 Å2
2--2.93 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.87→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8705 0 40 618 9363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129042
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168450
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.81712293
X-RAY DIFFRACTIONr_angle_other_deg0.4461.73619445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6951152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.747544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.222101469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21431
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210655
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021983
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_it6.5572.9214566
X-RAY DIFFRACTIONr_mcbond_other6.5542.9214566
X-RAY DIFFRACTIONr_mcangle_it9.8995.2385732
X-RAY DIFFRACTIONr_mcangle_other9.8995.2385733
X-RAY DIFFRACTIONr_scbond_it7.4153.1944476
X-RAY DIFFRACTIONr_scbond_other7.2673.1764449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.8155.7266520
X-RAY DIFFRACTIONr_long_range_B_refined24.11629.049322
X-RAY DIFFRACTIONr_long_range_B_other23.82828.489185
X-RAY DIFFRACTIONr_rigid_bond_restr3.097317492
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.917 Å
RfactorNum. reflection% reflection
Rfree0.348 399 -
Rwork0.276 7014 -
obs--92.67 %

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