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- PDB-7efa: Crystal structure of the complex between the C-terminal domain of... -

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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


Displacement of DNA glycosylase by APEX1 / adenine glycosylase / Cleavage of the damaged purine / MutSalpha complex binding / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / DNA N-glycosylase activity / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity ...Displacement of DNA glycosylase by APEX1 / adenine glycosylase / Cleavage of the damaged purine / MutSalpha complex binding / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / DNA N-glycosylase activity / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / negative regulation of necroptotic process / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / translesion synthesis / estrous cycle / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / liver regeneration / epithelial cell differentiation / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / positive regulation of DNA replication / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / nuclear estrogen receptor binding / male germ cell nucleus / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / base-excision repair / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / 4 iron, 4 sulfur cluster binding / chromatin organization / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / centrosome / chromatin binding / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / identical protein 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 / DNA glycosylase / Proliferating cell nuclear antigen signature 2. / 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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / : / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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

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

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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

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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)

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