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- PDB-8jzy: RPA70N-RAD9 fusion -

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Basic information

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


checkpoint clamp complex / protein localization to chromosome / DNA replication factor A complex / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / single-stranded telomeric DNA binding / DNA replication checkpoint signaling / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate ...checkpoint clamp complex / protein localization to chromosome / DNA replication factor A complex / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / single-stranded telomeric DNA binding / DNA replication checkpoint signaling / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / 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 / 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 / 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 / 3'-5' exonuclease activity / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / DNA damage checkpoint signaling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / cellular response to ionizing radiation / 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 / SH3 domain binding / DNA-templated DNA replication / Formation of Incision Complex in GG-NER / histone deacetylase 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 / 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 / protein kinase binding / enzyme binding / nucleoplasm / nucleus / metal ion binding / 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 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 / 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

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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: 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

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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 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


Mass: 18.015 Da / Num. of mol.: 100 / 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, sodium phosphate

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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

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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→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 )

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