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- PDB-4e54: Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimer... -

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Basic information

Entry
Database: PDB / ID: 4.0E+54
TitleDamaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair
Components
  • AP24 DNA complementary strand
  • AP24 DNA strand
  • DNA damage-binding protein 1
  • DNA damage-binding protein 2
KeywordsDNA BINDING PROTEIN/DNA / BETA BARREL / DOUBLE HELIX / DDB1:WD40 beta-barrel fold / DNA damage / DNA repair / Host-virus interactions / Protein ubiquitination / Proteosomal degradation / DNA BINDING PROTEIN-DNA complex
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 / site of DNA damage / cullin family protein binding / viral release from host cell / pyrimidine dimer repair / ectopic germ cell programmed cell death / positive regulation of viral genome replication / protein autoubiquitination / response to UV / positive regulation of gluconeogenesis / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / 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 / protein polyubiquitination / 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 / cell junction / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / Ub-specific processing proteases / DNA repair / apoptotic process / DNA damage response / chromatin / 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
30s Ribosomal Protein S18 - #30 / DNA damage-binding protein 2 / DNA polymerase; domain 1 - #910 / 30s Ribosomal Protein S18 / 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 ...30s Ribosomal Protein S18 - #30 / DNA damage-binding protein 2 / DNA polymerase; domain 1 - #910 / 30s Ribosomal Protein S18 / 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 / Few Secondary Structures / Irregular / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsYeh, J.I. / Du, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair.
Authors: Yeh, J.I. / Levine, A.S. / Du, S. / Chinte, U. / Ghodke, H. / Wang, H. / Shi, H. / Hsieh, C.L. / Conway, J.F. / Van Houten, B. / Rapic-Otrin, V.
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_leaving_atom_flag / _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
F: AP24 DNA strand
G: AP24 DNA complementary strand


Theoretical massNumber of molelcules
Total (without water)192,0224
Polymers192,0224
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-33 kcal/mol
Surface area70230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.736, 70.877, 191.448
Angle α, β, γ (deg.)90.00, 99.68, 90.00
Int Tables number4
Space group name H-MP1211

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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: 128478.914 Da / Num. of mol.: 1 / Fragment: DNA DAMAGE-BINDING PROTEIN 1 (DDB1; p127) / Mutation: NT-His10-DDB1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, DDB1_HUMAN, Q16531, XAP1 / Plasmid: pBlueBac4.5/V5-His NT-His10-DDB1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein DNA damage-binding protein 2 / DDB p48 subunit / DDBb / Damage-specific DNA-binding protein 2 / UV-damaged DNA-binding protein 2 / UV-DDB 2


Mass: 48928.906 Da / Num. of mol.: 1 / Fragment: DNA DAMAGE-BINDING PROTEIN 2 (DDB2; p48) / Mutation: N-FLAG-DDB2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB2, DDB2_HUMAN, Q92466 / Plasmid: pBlueBac4.5/V5-His NT-FLAG-DDB2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92466
#3: DNA chain AP24 DNA strand


Mass: 7424.801 Da / Num. of mol.: 1 / Fragment: AP24 DNA strand / Source method: obtained synthetically
Details: Synthetic single stranded 24-oligodeoxynucleotides with complementary strand sequence: 5-TGACTGTATGATGACGATGCTGAC-3
#4: DNA chain AP24 DNA complementary strand


Mass: 7189.646 Da / Num. of mol.: 1 / Fragment: AP24 DNA complementary strand / Source method: obtained synthetically
Details: Synthetic single stranded oligodeoxynucleotides with a central tetrahydrofuran abasic site mimic (3DR) on coding strand with sequence: 5-GTCAGCATCG(3DR)CATCATACAGTCA-3

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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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24- ...Details: 20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24-bpr with a central abasic site mimic., VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: monochromators
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 47108 / % possible obs: 89.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 25.22 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.1 / Net I/σ(I): 12.28
Reflection shellResolution: 2.85→2.96 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 7.7 / Num. unique all: 3545 / Rsym value: 0.321 / % possible all: 67.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3EI2

3ei2


Resolution: 2.85→33.315 Å / SU ML: 0.79 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 2.7 / Phase error: 24.09 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 1931 4.99 %Random
Rwork0.2331 ---
all0.2582 47108 --
obs0.2355 38719 81.03 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 299.989 Å2 / ksol: 0.265 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.9366 Å2-0 Å2-2.0964 Å2
2---25.9332 Å2-0 Å2
3----21.89 Å2
Refine analyzeLuzzati sigma a free: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.85→33.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11998 977 0 0 12975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513336
X-RAY DIFFRACTIONf_angle_d1.35418288
X-RAY DIFFRACTIONf_dihedral_angle_d20.0934964
X-RAY DIFFRACTIONf_chiral_restr0.1022075
X-RAY DIFFRACTIONf_plane_restr0.0062196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.92120.2865770.24721432X-RAY DIFFRACTION45
2.9212-3.00020.32541010.24682029X-RAY DIFFRACTION63
3.0002-3.08840.31931320.23822436X-RAY DIFFRACTION75
3.0884-3.1880.26631400.23762616X-RAY DIFFRACTION82
3.188-3.30180.28591430.23152741X-RAY DIFFRACTION85
3.3018-3.43390.30091420.23212756X-RAY DIFFRACTION86
3.4339-3.590.26431440.22992810X-RAY DIFFRACTION86
3.59-3.77910.26251510.22922773X-RAY DIFFRACTION87
3.7791-4.01550.30321500.23252860X-RAY DIFFRACTION88
4.0155-4.32490.26481510.22762804X-RAY DIFFRACTION87
4.3249-4.7590.27011490.22692908X-RAY DIFFRACTION89
4.759-5.44510.28741550.21322895X-RAY DIFFRACTION89
5.4451-6.85040.25931470.23982879X-RAY DIFFRACTION88
6.8504-33.31720.27851490.24712849X-RAY DIFFRACTION84
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)
10.0043-0.00020.00020.0046-0.0012-0.00020.0140.00630.0074-0.0397-0.0241-0.01520.0052-0.0051-0.00050.36890.0691-0.02440.3524-0.06420.457322.510713.298630.7426
2-0.0004-0.0008-0.00120.0020.00310.0030.0050.0023-0.00470.00360.00320.00180.00220.00360.0037-0.011-0.0341-0.0241-0.02680.00760.013922.844-3.182540.1019
30.2961-0.1794-0.07340.1491-0.00850.0997-0.03440.056-0.1462-0.04410.00890.08540.0672-0.03290.02560.0414-0.00210.01090.0854-0.0068-0.014711.676-21.369621.7459
40.1036-0.04820.01730.03280.01660.0496-0.1015-0.06090.22540.09960.01510.0942-0.2105-0.06250.1331-0.22430.11180.0238-0.17270.0455-0.12569.1752-1.477369.0253
50.00690.00270.01360.00910.00880.0135-0.00490.0339-0.0267-0.05440.02320.04790.01030.00690.00120.155-0.0460.00720.11990.03030.136914.4057-27.2513-1.6698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and ((resseq 26:70))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 71:103))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 104:421))
4X-RAY DIFFRACTION4chain 'A'
5X-RAY DIFFRACTION5(chain 'G') or (chain 'F')

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