[English] 日本語
Yorodumi
- PDB-8jzv: RPA70N-ETAA1 fusion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jzv
TitleRPA70N-ETAA1 fusion
Components
  • Ewing's tumor-associated antigen 1
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsDNA BINDING PROTEIN / RPA / 70N / ETAA1
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / regulation of DNA damage checkpoint / protein localization to site of double-strand break / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / mitotic G2/M transition checkpoint / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) ...protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / regulation of DNA damage checkpoint / protein localization to site of double-strand break / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / mitotic G2/M transition checkpoint / 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 / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / replication fork processing / nuclear replication fork / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / telomere maintenance via telomerase / mismatch repair / SUMOylation of DNA damage response and repair proteins / Activation of ATR in response to replication stress / telomere maintenance / protein serine/threonine kinase activator activity / 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 / positive regulation of protein serine/threonine kinase activity / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / base-excision repair / G2/M DNA damage checkpoint / PML body / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Meiotic recombination / DNA-templated DNA replication / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / DNA replication / chromosome, telomeric region / DNA repair / DNA damage response / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Ewing's tumour-associated antigen 1 / Ewing's tumour-associated antigen 1 homologue / 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 ...Ewing's tumour-associated antigen 1 / Ewing's tumour-associated antigen 1 homologue / 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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit / Ewing's tumor-associated antigen 1
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: Ewing's tumor-associated antigen 1


Theoretical massNumber of molelcules
Total (without water)16,0312
Polymers16,0312
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-6 kcal/mol
Surface area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.209, 50.209, 94.526
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 / 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 Ewing's tumor-associated antigen 1 / Ewing's tumor-associated antigen 16


Mass: 2843.960 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETAA1, ETAA16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY74
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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, Ammonium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.5→39.5 Å / Num. obs: 42672 / % possible obs: 99.96 % / Redundancy: 9.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.05676 / Net I/σ(I): 26.24
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.2213 / Num. unique obs: 2702 / CC1/2: 0.981 / Rpim(I) all: 0.07917

-
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→39.5 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 2151 5.04 %
Rwork0.1837 --
obs0.1846 42672 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 139 1160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.261
X-RAY DIFFRACTIONf_dihedral_angle_d5.49138
X-RAY DIFFRACTIONf_chiral_restr0.077170
X-RAY DIFFRACTIONf_plane_restr0.012180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.23061320.20682702X-RAY DIFFRACTION100
1.54-1.570.24071470.18432711X-RAY DIFFRACTION100
1.57-1.620.22731480.18742727X-RAY DIFFRACTION100
1.62-1.660.21361320.18762692X-RAY DIFFRACTION100
1.66-1.720.23411600.21132657X-RAY DIFFRACTION100
1.72-1.780.19321440.18712706X-RAY DIFFRACTION100
1.78-1.850.22391380.18642733X-RAY DIFFRACTION100
1.85-1.930.22351500.18782673X-RAY DIFFRACTION100
1.93-2.040.19541160.18622731X-RAY DIFFRACTION100
2.04-2.160.20251750.18262659X-RAY DIFFRACTION100
2.16-2.330.21721720.18192697X-RAY DIFFRACTION100
2.33-2.560.18311520.18932669X-RAY DIFFRACTION100
2.57-2.940.23771040.19832746X-RAY DIFFRACTION100
2.94-3.70.17611400.17832715X-RAY DIFFRACTION100
3.7-39.50.18561410.17032703X-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)
12.77060.08340.34222.57190.08121.775-0.0107-0.0553-0.14240.12080.06110.07580.08150.0293-0.04890.1475-0.01750.00580.11890.00590.108719.5132-21.04426.646
25.5841-2.4811.19174.3122-0.17431.36220.02480.0981-0.21090.3290.0577-0.08810.09310.37520.00120.2527-0.0193-0.04340.232-0.02290.180229.5133-16.881412.8657
31.6580.47370.90141.42320.69531.27460.03610.0461-0.1973-0.12680.03-0.1356-0.0109-0.0562-0.05610.1426-0.0141-0.00010.1215-0.00110.128417.2461-26.11231.0324
41.4116-0.43110.13442.7601-0.00731.328-0.0081-0.02110.09710.06130.0006-0.1698-0.02570.08370.00760.1427-0.0392-0.00510.1318-0.00630.135324.5265-17.93955.4702
52.8769-0.2461-0.67562.6821-0.75512.0081-0.0289-0.09670.11510.46250.04660.42660.2428-0.2022-0.00350.2165-0.01480.0770.2405-0.04880.192411.3875-14.060512.8672
64.7094-1.91480.53613.8171-0.99492.438-0.4782-1.354-1.03071.24610.16820.5157-0.3819-0.41560.33910.5797-0.02940.0740.64320.03030.485811.3125-30.744914.5614
74.7290.10221.32133.4448-0.91343.1396-0.1911-0.6916-1.59050.11790.1406-0.0931.2531-0.08590.08360.4053-0.019-0.03760.27220.0930.530718.7682-36.375910.131
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 108 )
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 119 )
6X-RAY DIFFRACTION6chain 'B' and (resid 599 through 603 )
7X-RAY DIFFRACTION7chain 'B' and (resid 604 through 615 )

+
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