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- PDB-3i7k: Crystal Structure of DDB1 in Complex with the H-Box Motif of WHX -

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Basic information

Entry
Database: PDB / ID: 3i7k
TitleCrystal Structure of DDB1 in Complex with the H-Box Motif of WHX
Components
  • DNA damage-binding protein 1
  • X protein
KeywordsPROTEIN BINDING/VIRAL PROTEIN / DDB1 / HBV / X protein / H-Box Motif / Cytoplasm / DNA damage / DNA repair / DNA-binding / Host-virus interaction / Nucleus / Phosphoprotein / Polymorphism / Ubl conjugation / Ubl conjugation pathway / Activator / Apoptosis / Mitochondrion / Transcription / Transcription regulation / PROTEIN BINDING-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


: / symbiont-mediated arrest of host cell cycle during G2/M transition / 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 ...: / symbiont-mediated arrest of host cell cycle during G2/M transition / 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 / host cell mitochondrion / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / positive regulation of gluconeogenesis / viral genome replication / 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 / DNA-templated transcription / apoptotic process / DNA damage response / host cell nucleus / 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
Transactivation protein X / Trans-activation protein X / 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 ...Transactivation protein X / Trans-activation protein X / 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 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein X / DNA damage-binding protein 1 / Protein X
Similarity search - Component
Biological speciesHomo sapiens (human)
Woodchuck hepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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: X protein


Theoretical massNumber of molelcules
Total (without water)129,0592
Polymers129,0592
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-8 kcal/mol
Surface area48980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.081, 132.215, 184.001
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 / 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.: 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
#2: Protein/peptide X protein


Mass: 1658.880 Da / Num. of mol.: 1 / Fragment: Residues 86-99 / Source method: obtained synthetically / Source: (synth.) Woodchuck hepatitis B virus / References: UniProt: Q89246, UniProt: P03167*PLUS
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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005 M 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: 2.8→46.03 Å / Num. all: 38728 / Num. obs: 35137 / % possible obs: 90.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.4
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2285 / % possible all: 94.6

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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: 2.8→46.03 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.888 / SU B: 14.606 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.679 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1851 5 %RANDOM
Rwork0.23 ---
all0.252 38728 --
obs0.232 35137 94.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---1.36 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8843 0 0 0 8843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229007
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.96412200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10451123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38724.732410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.377151589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5061549
X-RAY DIFFRACTIONr_chiral_restr0.1080.21402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026733
X-RAY DIFFRACTIONr_nbd_refined0.2510.24180
X-RAY DIFFRACTIONr_nbtor_refined0.320.25969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2310
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.25
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 128 -
Rwork0.339 2285 -
obs-2285 85.23 %

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