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- PDB-8jzv: RPA70N-ETAA1 fusion -

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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 / lateral element / regulation of DNA damage checkpoint / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / mitotic G2/M transition checkpoint ...protein localization to chromosome / DNA replication factor A complex / lateral element / regulation of DNA damage checkpoint / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / 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 / nuclear replication fork / replication fork processing / hemopoiesis / Presynaptic phase of homologous DNA pairing and strand exchange / site of DNA damage / positive regulation of protein serine/threonine kinase activity / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / HSF1 activation / telomere maintenance via telomerase / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / homeostasis of number of cells within a tissue / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / protein serine/threonine kinase activator activity / meiotic cell cycle / male germ cell nucleus / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / PML body / G2/M DNA damage checkpoint / 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 / in utero embryonic development / damaged DNA binding / chromosome, telomeric region / DNA replication / DNA repair / positive regulation of cell population proliferation / DNA damage response / chromatin binding / zinc ion binding / nucleoplasm / nucleus / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium chloride

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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

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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 )

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