[English] 日本語
Yorodumi
- PDB-4e5z: Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e5z
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 / PROTEIN-DNA COMPLEX / DOUBLE HELIX / 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 / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / WD40-repeat domain binding ...positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / WD40-repeat domain binding / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / response to UV / negative regulation of adipose tissue development / regulation of cellular response to stress / viral release from host cell / cullin family protein binding / regulation of DNA-templated DNA replication initiation / positive regulation of viral genome replication / positive regulation of gluconeogenesis / protein autoubiquitination / regulation of embryonic development / replication fork processing / site of DNA damage / TP53 Regulates Transcription of DNA Repair Genes / proteasomal protein catabolic process / epigenetic regulation of gene expression / nucleotide-excision repair / regulation of autophagy / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / cell population proliferation / 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 / protein polyubiquitination / Formation of Incision Complex in GG-NER / positive regulation of protein catabolic process / cellular response to UV / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / regulation of cell population proliferation / rhythmic process / site of double-strand break / Neddylation / spermatogenesis / ubiquitin-dependent protein catabolic process / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein-macromolecule adaptor activity / chromosome, telomeric region / protein ubiquitination / Ub-specific processing proteases / DNA repair / DNA damage response / nucleolus / protein-containing complex binding / chromatin / protein-containing complex / DNA binding / : / 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 / : / 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 ...30s Ribosomal Protein S18 - #30 / DNA damage-binding protein 2 / DNA polymerase; domain 1 - #910 / 30s Ribosomal Protein S18 / : / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Few Secondary Structures / Irregular / DNA polymerase; domain 1 / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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: 3.22 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 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 13, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)192,1524
Polymers192,1524
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-45 kcal/mol
Surface area74300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.418, 76.504, 389.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
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
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-DDB1pBlueBac4.5/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: 49059.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB2 / Plasmid: pBlueBac4.5/V5-HisNT-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 / 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 / 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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D
DetectorType: MARMOSAIC 225 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 wavelengthRelative weight: 1
ReflectionResolution: 3.2→41.093 Å / Num. all: 36260 / Num. obs: 33928 / % possible obs: 77.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 38.09 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.105 / Net I/σ(I): 10.9
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.358 / % possible all: 77.8

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EI2

3ei2


Resolution: 3.22→41.093 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU ML: 0.44 / σ(F): 0 / Phase error: 30.96 / Stereochemistry target values: MLHL
Details: THE MODEL WAS REFINED USING ITERATIVE CYCLES OF TLS AND RESTRAINED REFINEMENT (INCLUDING SECONDARY STRUCTURE, GEOMETRY, AND TORSION ANGLE RESTRAINTS) THROUGH PHENIX. CAREFUL INSPECTION OF ...Details: THE MODEL WAS REFINED USING ITERATIVE CYCLES OF TLS AND RESTRAINED REFINEMENT (INCLUDING SECONDARY STRUCTURE, GEOMETRY, AND TORSION ANGLE RESTRAINTS) THROUGH PHENIX. CAREFUL INSPECTION OF WEIGHTED AND UNWEIGHTED MAPS, IN PARTICULAR, THE DIFFERENCE FOURIER MAPS, AFTER EACH REFINEMENT ROUND VERIFIED CORRECTNESS OF REGIONS MODIFIED OR EXTENDED IN THE PREVIOUS CYCLE. PROGRAMMATIC DIFFERENCES IN THE APPLICATION AND SCALING OF TLS PARAMETERS MAY RESULT IN VARIATIONS IN THE MAPS CALCULATED USING THE SF DIRECTLY DOWNLOADED FROM THE DATABASE. CALCULATING STRUCTURE FACTORS (SF) USING MODEL COORDINATES AND THERMAL PARAMETERS FROM THE DEPOSITED PDB FILES IN PHENIX WILL REPRODUCE THE MAPS AND CONFORMATIONAL FEATURES DESCRIBED BY THE AUTHORS IN THE CITATION.
RfactorNum. reflection% reflection
Rfree0.284 1690 4.98 %
Rwork0.2277 --
obs0.2304 33928 93.64 %
all-35809 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 185.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.57 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 3.22→41.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12008 977 0 0 12985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113343
X-RAY DIFFRACTIONf_angle_d2.03618303
X-RAY DIFFRACTIONf_dihedral_angle_d26.2128046
X-RAY DIFFRACTIONf_chiral_restr0.1012077
X-RAY DIFFRACTIONf_plane_restr0.0112198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2201-3.31480.38931040.2722032X-RAY DIFFRACTION72
3.3148-3.42180.38421180.27172499X-RAY DIFFRACTION89
3.4218-3.5440.32931500.26672611X-RAY DIFFRACTION93
3.544-3.68580.32281390.26422676X-RAY DIFFRACTION95
3.6858-3.85340.35081400.26962766X-RAY DIFFRACTION97
3.8534-4.05640.33741480.26042747X-RAY DIFFRACTION97
4.0564-4.31030.30341370.23962790X-RAY DIFFRACTION98
4.3103-4.64270.28461510.20952750X-RAY DIFFRACTION97
4.6427-5.10910.22311470.19652816X-RAY DIFFRACTION97
5.1091-5.84660.26231420.22132771X-RAY DIFFRACTION96
5.8466-7.35920.28741580.2672803X-RAY DIFFRACTION96
7.3592-41.09620.2591560.19772977X-RAY DIFFRACTION96
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)
10.063-0.01770.00940.1083-0.01410.03280.02460.0179-0.0124-0.0609-0.01990.03140.0280.01390.28020.072-0.0053-0.04960.12190.16660.117631.0584-26.598-70.5307
20.0085-0.00470.00510.0029-0.00380.0058-0.0210.00740.02270.0232-0.0248-0.0282-0.02480.037-0.24630.0876-0.0377-0.05630.09240.08530.093245.7443-31.9382-25.5884
30.084-0.0222-0.05210.00590.01330.03140.0029-0.05060.02060.0586-0.0021-0.0174-0.07970.06390.04370.42920.0257-0.08960.2030.07730.244657.3005-32.45180.87
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3(chain 'G') or (chain 'F')

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more