[English] 日本語
Yorodumi
- PDB-7efa: Crystal structure of the complex between the C-terminal domain of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7efa
TitleCrystal structure of the complex between the C-terminal domain of mouse MUTYH and human PCNA
Components
  • Adenine DNA glycosylase
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA replication / DNA repair
Function / homology
Function and homology information


adenine/guanine mispair binding / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / adenine glycosylase / MutSalpha complex binding / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication ...adenine/guanine mispair binding / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / adenine glycosylase / MutSalpha complex binding / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / DNA N-glycosylase activity / Processive synthesis on the lagging strand / PCNA complex / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / negative regulation of necroptotic process / replisome / oxidized purine DNA binding / response to L-glutamate / histone acetyltransferase binding / leading strand elongation / DNA polymerase processivity factor activity / replication fork processing / G1/S-Specific Transcription / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / translesion synthesis / response to cadmium ion / DNA polymerase binding / base-excision repair, gap-filling / positive regulation of DNA repair / epithelial cell differentiation / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / base-excision repair / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / 4 iron, 4 sulfur cluster binding / heart development / response to oxidative stress / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / centrosome / chromatin binding / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus
Similarity search - Function
Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif ...Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / Proliferating cell nuclear antigen signature 2. / DNA glycosylase / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Adenine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNakamura, T. / Nakabeppu, Y. / Yamagata, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer.
Authors: Nakamura, T. / Okabe, K. / Hirayama, S. / Chirifu, M. / Ikemizu, S. / Morioka, H. / Nakabeppu, Y. / Yamagata, Y.
History
DepositionMar 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Adenine DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)49,9532
Polymers49,9532
Non-polymers00
Water181
1
A: Proliferating cell nuclear antigen
B: Adenine DNA glycosylase

A: Proliferating cell nuclear antigen
B: Adenine DNA glycosylase

A: Proliferating cell nuclear antigen
B: Adenine DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)149,8596
Polymers149,8596
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area9300 Å2
ΔGint-51 kcal/mol
Surface area59150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.780, 87.780, 124.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

-
Components

#1: Protein Proliferating cell nuclear antigen / / PCNA / Cyclin


Mass: 28795.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P12004
#2: Protein Adenine DNA glycosylase / MutY homolog / mMYH


Mass: 21157.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mutyh, Myh / Production host: Escherichia coli (E. coli) / References: UniProt: Q99P21, adenine glycosylase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG8000, imidazole

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→36.4 Å / Num. obs: 14970 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 92.86 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 29.9
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 1.19 / Num. unique obs: 11997

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UL1

1ul1


Resolution: 2.7→36.4 Å / SU ML: 0.327 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.8465 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2864 749 5.01 %
Rwork0.2347 14189 -
obs0.2373 14938 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 122.79 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 0 1 2852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242897
X-RAY DIFFRACTIONf_angle_d0.49833944
X-RAY DIFFRACTIONf_chiral_restr0.0432466
X-RAY DIFFRACTIONf_plane_restr0.0031519
X-RAY DIFFRACTIONf_dihedral_angle_d8.47951759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.33741540.28272812X-RAY DIFFRACTION99.93
2.91-3.20.39511090.29242860X-RAY DIFFRACTION99.97
3.2-3.660.30551830.27222806X-RAY DIFFRACTION99.9
3.66-4.620.26741340.22542868X-RAY DIFFRACTION100
4.62-36.40.27431690.21682843X-RAY DIFFRACTION99.7
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)
16.17283886294-2.872265647871.450286720324.9731789534-0.6146829261122.48135998131-0.212350923794-0.06801442572121.303670988870.2277291712440.0271905042479-0.997984335092-0.4098860184330.3190354633640.1049134147510.443039255921-0.1221472784310.01529629947290.4204731426960.01539085511780.6755260892916.865020116-31.8831330148-12.7156717303
21.36139355018-0.7635721213240.7966337152574.013139447561.308075704991.326142293760.265040958559-1.13932887488-0.02052425737840.562383893672-0.4948741634790.959226551678-0.908164630231-0.493317744442-0.2429126853871.07499440778-0.1672605573250.2574578008831.88599837015-0.04308137198570.3978049106622.40914094991-27.0268356946-49.089508223
39.487846925684.01186234364-1.892547233146.477181822593.069348834377.922585287750.464267594191.131519331571.51681709873-1.13487742514-0.372789945431-1.67445472521-2.587739899941.221419186140.1278713239691.57105355906-0.107556230870.5591529338331.312447781010.5827267191221.4866914498614.0146035527-17.9844397575-27.3692854143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 256)
2X-RAY DIFFRACTION2(chain 'B' and resid 336 through 469)
3X-RAY DIFFRACTION3(chain 'B' and resid 490 through 503)

+
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