[English] 日本語
Yorodumi
- PDB-3k75: X-ray crystal structure of reduced XRCC1 bound to DNA pol beta ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k75
TitleX-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain
Components
  • DNA polymerase beta
  • DNA repair protein XRCC1
KeywordsDNA BINDING PROTEIN / allosteric disulfide / XRCC1 / pol beta / DNA damage / DNA repair / Nucleus / Phosphoprotein / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Lyase / Magnesium / Metal-binding / Methylation / Nucleotidyltransferase / Transferase / DNA-BINDING PROTEIN
Function / homology
Function and homology information


3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway ...3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / ADP-D-ribose modification-dependent protein binding / somatic diversification of immunoglobulins / negative regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / Ub-specific processing proteases / positive regulation of single strand break repair / cerebellum morphogenesis / voluntary musculoskeletal movement / single strand break repair / HDR through MMEJ (alt-NHEJ) / response to hydroperoxide / Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / pyrimidine dimer repair / 5'-deoxyribose-5-phosphate lyase activity / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / base-excision repair, gap-filling / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / hippocampus development / Gap-filling DNA repair synthesis and ligation in GG-NER / response to gamma radiation / spindle microtubule / base-excision repair / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / microtubule binding / neuron apoptotic process / in utero embryonic development / microtubule / response to ethanol / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / chromosome, telomeric region / response to hypoxia / DNA replication / lyase activity / inflammatory response / response to xenobiotic stimulus / apoptotic process / DNA damage response / chromatin / nucleolus / enzyme binding / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm ...DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Galactose-binding domain-like / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / Galactose-binding-like domain superfamily / DNA polymerase; domain 1 / Jelly Rolls / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase beta / DNA repair protein XRCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.95 Å
AuthorsCuneo, M.J. / London, R.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity.
Authors: Cuneo, M.J. / London, R.E.
History
DepositionOct 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_keywords / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: DNA repair protein XRCC1
C: DNA repair protein XRCC1
D: DNA polymerase beta
E: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)100,7934
Polymers100,7934
Non-polymers00
Water00
1
B: DNA repair protein XRCC1
D: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)50,3972
Polymers50,3972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8 kcal/mol
Surface area19560 Å2
MethodPISA
2
C: DNA repair protein XRCC1
E: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)50,3972
Polymers50,3972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-8 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.770, 44.050, 152.770
Angle α, β, γ (deg.)90.000, 107.210, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12D
22E

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUSERSERBA6 - 1406 - 140
21LEULEUSERSERCB6 - 1406 - 140
12SERSERPROPRODC95 - 3306 - 241
22SERSERPROPROED95 - 3306 - 241

NCS ensembles :
ID
1
2

-
Components

#1: Protein DNA repair protein XRCC1 / X-ray repair cross-complementing protein 1


Mass: 21060.527 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1 to 183)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: XRCC1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P18887
#2: Protein DNA polymerase beta


Mass: 29336.111 Da / Num. of mol.: 2 / Fragment: UNP residues 91 to 335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: Rattus / Gene: Polb / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P06766, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-25% PEG 3350, 0.2-0.3M Tri-potassium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→25 Å / Num. obs: 19123 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.334 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.7
Reflection shellResolution: 2.95→3.03 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 4872 / Num. unique all: 1376 / Num. unique obs: 1376 / % possible all: 99.6

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.95→24.47 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.813 / Occupancy max: 1 / Occupancy min: 0 / SU B: 49.195 / SU ML: 0.417 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.295 957 5 %RANDOM
Rwork0.242 ---
all0.245 ---
obs0.245 19123 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 137.8 Å2 / Biso mean: 51.723 Å2 / Biso min: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20.35 Å2
2--0.48 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.95→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 0 0 6282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226481
X-RAY DIFFRACTIONr_bond_other_d00.025836
X-RAY DIFFRACTIONr_angle_refined_deg0.8421.968747
X-RAY DIFFRACTIONr_angle_other_deg0.789313618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41423.576316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.602151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7171559
X-RAY DIFFRACTIONr_chiral_restr0.0720.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217239
X-RAY DIFFRACTIONr_gen_planes_other00.021334
X-RAY DIFFRACTIONr_mcbond_it2.5441.53986
X-RAY DIFFRACTIONr_mcbond_other1.3251.51617
X-RAY DIFFRACTIONr_mcangle_it4.68226454
X-RAY DIFFRACTIONr_scbond_it3.25132495
X-RAY DIFFRACTIONr_scangle_it4.5144.52293
X-RAY DIFFRACTIONr_rigid_bond_restr4.119312317
X-RAY DIFFRACTIONr_sphericity_bonded11.941312185
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1904MEDIUM POSITIONAL0.70.5
1B1904MEDIUM THERMAL6.792
2D3696MEDIUM POSITIONAL0.320.5
2D3696MEDIUM THERMAL3.962
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 68 -
Rwork0.355 1287 -
all-1355 -
obs-1326 100 %

+
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