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- PDB-8zsw: Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin ... -

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Basic information

Entry
Database: PDB / ID: 8zsw
TitleCrystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex
ComponentsDNA damage-binding protein 1
KeywordsPROTEIN BINDING / E3 ubiquitin ligase component / DDB1
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 / positive regulation of protein catabolic process / Dual incision in TC-NER / 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
ACETATE ION / DNA damage-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLee, J. / Gil, Y. / Jeong, Y.R. / Jo, I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentKK2432-10 Korea, Republic Of
CitationJournal: To Be Published
Title: Improved-Resolution Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex
Authors: Jo, I. / Gil, Y. / Jeong, Y.R. / Lee, J.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA damage-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1902
Polymers129,1311
Non-polymers591
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area46940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.590, 118.310, 120.970
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 / 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: 129130.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES (pH 6.5), 0.1M sodium acetate, 27%(w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.25→29.73 Å / Num. obs: 66888 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.02606 / Net I/σ(I): 17.24
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 2.88 / Num. unique obs: 6617 / CC1/2: 0.814 / CC star: 0.947 / Rpim(I) all: 0.3137 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→29.73 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 3345 5 %
Rwork0.1884 --
obs0.1905 66881 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8691 0 4 298 8993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038922
X-RAY DIFFRACTIONf_angle_d0.53412095
X-RAY DIFFRACTIONf_dihedral_angle_d4.5121201
X-RAY DIFFRACTIONf_chiral_restr0.0451393
X-RAY DIFFRACTIONf_plane_restr0.0041564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.36071390.27922631X-RAY DIFFRACTION100
2.28-2.320.30431370.26872604X-RAY DIFFRACTION100
2.32-2.350.3281370.25732610X-RAY DIFFRACTION100
2.35-2.390.29511380.24192631X-RAY DIFFRACTION100
2.39-2.430.27551380.24142619X-RAY DIFFRACTION100
2.43-2.480.30811380.23792616X-RAY DIFFRACTION100
2.48-2.520.27971380.23692618X-RAY DIFFRACTION100
2.52-2.580.31071390.22772638X-RAY DIFFRACTION100
2.58-2.630.29291380.23252631X-RAY DIFFRACTION100
2.63-2.690.29661380.23812623X-RAY DIFFRACTION100
2.69-2.760.29321370.23812600X-RAY DIFFRACTION100
2.76-2.830.2781390.24512635X-RAY DIFFRACTION99
2.83-2.920.27821390.23812638X-RAY DIFFRACTION100
2.92-3.010.27541380.22242626X-RAY DIFFRACTION100
3.01-3.120.28281390.21972637X-RAY DIFFRACTION100
3.12-3.240.26041390.22172650X-RAY DIFFRACTION100
3.24-3.390.25341400.2072657X-RAY DIFFRACTION100
3.39-3.570.26211390.192640X-RAY DIFFRACTION100
3.57-3.790.21631410.18012669X-RAY DIFFRACTION100
3.79-4.090.2121410.16752680X-RAY DIFFRACTION100
4.09-4.50.19421400.14552674X-RAY DIFFRACTION100
4.5-5.140.13791430.13282701X-RAY DIFFRACTION100
5.14-6.470.20661420.17122703X-RAY DIFFRACTION99
6.47-29.730.19231480.17112805X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1754-0.2915-0.18681.43520.00421.2572-0.02230.1437-0.3389-0.3117-0.0762-0.17560.15910.17990.09690.4029-0.01890.04260.34060.00880.40437.701437.0192-36.658
20.8144-0.3918-0.3892.23461.66811.9213-0.1031-0.44230.32920.22640.1210.09150.03890.1617-0.01370.35960.0232-0.0420.5581-0.0740.5075-0.240358.515512.6149
30.86360.09880.05492.1618-0.47490.9306-0.03360.0390.02970.07620.02190.17490.0658-0.1115-0.00750.346-0.01980.02420.3876-0.01970.2869-15.148227.8787-10.8752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 307 )
2X-RAY DIFFRACTION2chain 'A' and (resid 308 through 708 )
3X-RAY DIFFRACTION3chain 'A' and (resid 709 through 1140 )

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