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- PDB-3i8e: Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A -

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Basic information

Entry
Database: PDB / ID: 3i8e
TitleCrystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A
Components
  • DNA damage-binding protein 1
  • WD repeat-containing protein 42A
KeywordsPROTEIN BINDING / DDB1 / WDR42A / H326 / DCAF8 / H-Box Motif / DNA damage / DNA repair / DNA-binding / Host-virus interaction / Nucleus / Phosphoprotein / Ubl conjugation pathway / WD repeat
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 / positive regulation of gluconeogenesis / post-translational protein modification / 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 / mitochondrion / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / 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 / DDB1- and CUL4-associated factor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLi, T. / Robert, E.I. / Breugel, P.C.V. / Strubin, M. / Zheng, N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: A promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery.
Authors: Li, T. / Robert, E.I. / van Breugel, P.C. / Strubin, M. / Zheng, N.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: DNA damage-binding protein 1
C: WD repeat-containing protein 42A
D: WD repeat-containing protein 42A


Theoretical massNumber of molelcules
Total (without water)257,6834
Polymers257,6834
Non-polymers00
Water0
1
A: DNA damage-binding protein 1
C: WD repeat-containing protein 42A


Theoretical massNumber of molelcules
Total (without water)128,8412
Polymers128,8412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area48710 Å2
MethodPISA
2
B: DNA damage-binding protein 1
D: WD repeat-containing protein 42A


Theoretical massNumber of molelcules
Total (without water)128,8412
Polymers128,8412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-6 kcal/mol
Surface area48950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.138, 133.815, 183.999
Angle α, β, γ (deg.)90.00, 90.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA damage-binding protein 1 / Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 subunit / DNA ...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: 127399.766 Da / Num. of mol.: 2
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
#2: Protein/peptide WD repeat-containing protein 42A


Mass: 1441.633 Da / Num. of mol.: 2 / Fragment: Residues 153-165 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5TAQ9
Sequence detailsMUTATIONS OCCURRED DURING THE CLONING OF DDB1

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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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0,1.005
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.0051
ReflectionResolution: 3.4→49.15 Å / Num. all: 38723 / Num. obs: 35597 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 10.7
Reflection shellResolution: 3.4→3.488 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2592 / % possible all: 92.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B5M

2b5m


Resolution: 3.4→49.15 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.804 / SU B: 91.559 / SU ML: 0.674 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.861 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.338 1826 4.9 %RANDOM
Rwork0.26 ---
all0.304 38723 --
obs0.264 35597 87.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.285 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å20.11 Å2
2--1.83 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17652 0 0 0 17652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02217972
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.96624338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5352244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39624.73816
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.966153182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.68115100
X-RAY DIFFRACTIONr_chiral_restr0.080.22804
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213414
X-RAY DIFFRACTIONr_nbd_refined0.220.27938
X-RAY DIFFRACTIONr_nbtor_refined0.3070.211855
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2508
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.25
X-RAY DIFFRACTIONr_mcbond_it0.391.511482
X-RAY DIFFRACTIONr_mcangle_it0.701218106
X-RAY DIFFRACTIONr_scbond_it0.52937219
X-RAY DIFFRACTIONr_scangle_it0.9214.56232
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 119 -
Rwork0.327 2400 -
obs-2400 80.4 %
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)
12.8701-0.09110.04241.2209-0.07871.6593-0.0907-0.2824-0.39720.08060.16260.05510.2609-0.2006-0.07190.07870.0237-0.0413-0.04520.02990.01597.967210.146385.0251
21.2787-1.2472-0.20031.8099-0.36053.44850.2808-0.0917-0.46680.5214-0.0258-0.11181.16570.1798-0.2550.29170.0983-0.1123-0.0249-0.2510.037139.03840.282343.5039
32.8170.37221.14451.51530.30521.7091-0.1520.06030.3315-0.03940.1068-0.0359-0.30030.07370.0451-0.01650.02580.0073-0.13560.0149-0.001723.117636.771174.394
42.61790.1331-0.0191.191-0.2841.8247-0.03120.27060.3432-0.08980.13730.0853-0.1965-0.1647-0.10620.0783-0.04550.0413-0.07570.01010.0758-23.501762.70687.0723
50.91740.9815-0.39331.61780.7272.48930.17810.20430.2687-0.6196-0.0247-0.2183-1.03530.1252-0.15340.316-0.01180.09120.0149-0.162-0.05836.819572.453248.6955
62.6631-0.1872-0.98021.27280.08451.5406-0.1341-0.0668-0.40310.01640.0557-0.0630.17520.02270.07840.0121-0.0339-0.0056-0.15140.00860.0214-8.486836.02517.6994
7105.4908-58.3497-9.118786.796554.129164.05010.0186-0.88390.3711.08790.7899-0.3470.4265-0.175-0.80850.09280.0861-0.05040.0742-0.04150.111319.216735.250991.0702
873.03621.751810.2998124.991531.559429.358-0.44842.59150.44141.43770.81020.120.3645-0.1379-0.36180.0529-0.02650.04170.10750.19270.048217.039528.993785.9731
978.49327.802825.825372.483844.8268112.11492.2979-0.941-0.9611-0.2729-1.0174-0.27241.8822-0.2045-1.28050.12580.03780.06230.10570.01310.1343-12.262737.53221.2518
1073.4373-30.6331-11.014869.313220.539730.70940.341.32110.67410.075-1.1025-0.189-0.7407-1.30350.76240.0624-0.122-0.060.10280.1210.0725-14.804343.81896.4758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 395
2X-RAY DIFFRACTION2A396 - 709
3X-RAY DIFFRACTION3A710 - 1140
4X-RAY DIFFRACTION4B1 - 395
5X-RAY DIFFRACTION5B396 - 709
6X-RAY DIFFRACTION6B710 - 1140
7X-RAY DIFFRACTION7C153 - 159
8X-RAY DIFFRACTION8C160 - 165
9X-RAY DIFFRACTION9D153 - 159
10X-RAY DIFFRACTION10D160 - 165

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