[English] 日本語
Yorodumi
- PDB-8jzy: RPA70N-RAD9 fusion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jzy
TitleRPA70N-RAD9 fusion
Components
  • Cell cycle checkpoint control protein RAD9A
  • Replication protein A 70 kDa DNA-binding subunitDNA replication
KeywordsDNA BINDING PROTEIN / RPA / 70N / RAD9
Function / homology
Function and homology information


checkpoint clamp complex / protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / protein localization to site of double-strand break / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / single-stranded telomeric DNA binding ...checkpoint clamp complex / protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / protein localization to site of double-strand break / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / mitotic intra-S DNA damage checkpoint signaling / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / HSF1 activation / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / 3'-5' exonuclease activity / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / DNA damage checkpoint signaling / cellular response to ionizing radiation / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / DNA-templated DNA replication / PML body / Meiotic recombination / Formation of Incision Complex in GG-NER / histone deacetylase binding / SH3 domain binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / intrinsic apoptotic signaling pathway in response to DNA damage / site of double-strand break / single-stranded DNA binding / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / chromosome, telomeric region / DNA repair / DNA damage response / protein kinase binding / enzyme binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Rad9 / Rad9 / Rad9/Ddc1 / Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal ...Rad9 / Rad9 / Rad9/Ddc1 / Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / : / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit / Cell cycle checkpoint control protein RAD9A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFu, W.M. / Wu, Y.Y. / Zhou, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Elife / Year: 2023
Title: Structural characterization of human RPA70N association with DNA damage response proteins.
Authors: Wu, Y. / Fu, W. / Zang, N. / Zhou, C.
History
DepositionJul 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.pdbx_database_id_DOI ..._citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Replication protein A 70 kDa DNA-binding subunit
B: Cell cycle checkpoint control protein RAD9A


Theoretical massNumber of molelcules
Total (without water)15,3682
Polymers15,3682
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.041, 50.041, 93.255
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Replication protein A 70 kDa DNA-binding subunit / DNA replication / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein


Mass: 13187.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Production host: Escherichia coli (E. coli) / References: UniProt: P27694
#2: Protein/peptide Cell cycle checkpoint control protein RAD9A / hRAD9 / DNA repair exonuclease rad9 homolog A


Mass: 2180.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD9A / Production host: Escherichia coli (E. coli) / References: UniProt: Q99638, exodeoxyribonuclease III
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.5→25.26 Å / Num. obs: 41852 / % possible obs: 99.98 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0598 / Net I/σ(I): 20.11
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.5531 / Num. unique obs: 2679 / CC1/2: 0.927 / % possible all: 99.96

-
Processing

Software
NameVersionClassification
PHENIX(1.20rc1_4392: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XV4

7xv4


Resolution: 1.5→25.26 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 2092 5 %
Rwork0.1848 --
obs0.1856 41852 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 0 100 1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.049
X-RAY DIFFRACTIONf_dihedral_angle_d6.087140
X-RAY DIFFRACTIONf_chiral_restr0.062168
X-RAY DIFFRACTIONf_plane_restr0.008177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.24841360.25052679X-RAY DIFFRACTION100
1.53-1.570.22861000.21692685X-RAY DIFFRACTION100
1.57-1.620.23941620.2122625X-RAY DIFFRACTION100
1.62-1.660.24251360.2042651X-RAY DIFFRACTION100
1.66-1.720.20031040.21882689X-RAY DIFFRACTION100
1.72-1.780.24651480.23042624X-RAY DIFFRACTION100
1.78-1.850.23041590.20962656X-RAY DIFFRACTION100
1.85-1.930.23061580.18792619X-RAY DIFFRACTION100
1.93-2.040.21351440.18552638X-RAY DIFFRACTION100
2.04-2.160.18031360.18912678X-RAY DIFFRACTION100
2.16-2.330.20241480.19522605X-RAY DIFFRACTION100
2.33-2.560.17721400.19822631X-RAY DIFFRACTION100
2.56-2.930.21591540.19562674X-RAY DIFFRACTION100
2.94-3.690.18491460.17252629X-RAY DIFFRACTION100
3.7-25.260.18911210.16032677X-RAY DIFFRACTION100
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)
13.1571-0.22380.16785.34051.52132.76410.06760.0942-0.0449-0.0001-0.0126-0.11510.11490.0032-0.08120.1063-0.00290.00380.21080.00540.1276-16.693215.97198.9482
29.1441-1.11931.66882.89083.34775.22180.18870.603-0.56420.3012-0.28810.20930.4102-0.29120.15350.22520.0058-0.03770.3693-0.07150.2275-25.29868.95522.7758
36.8281.91360.94162.53980.40521.8040.0613-0.2536-0.57230.18660.0221-0.259-0.02080.1478-0.04530.15110.0146-0.00930.2108-0.02650.149-11.595915.395414.3321
44.4853-0.57340.76564.4159-1.4723.0420.08530.28490.0677-0.1453-0.03840.1553-0.06650.093-0.05040.14040.00220.01480.2277-0.03650.0855-20.615718.06657.2829
58.75331.33183.83293.2320.33662.97420.4204-0.27650.6177-0.23690.561-0.9255-0.1531.6244-0.740.6968-0.04120.12061.6006-0.39971.0101-6.40515.7564-1.4826
67.76641.6323-0.28868.2878-2.41759.66560.1667-0.2954-0.9540.5736-0.577-1.87811.10091.38640.45380.40970.13930.01340.5502-0.01570.7112-2.99749.24056.9874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 119 )
5X-RAY DIFFRACTION5chain 'B' and (resid 297 through 302 )
6X-RAY DIFFRACTION6chain 'B' and (resid 303 through 311 )

+
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