+Open data
-Basic information
Entry | Database: PDB / ID: 2pqa | ||||||
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Title | Crystal Structure of Full-length Human RPA 14/32 Heterodimer | ||||||
Components |
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Keywords | REPLICATION / RPA14/32 / ssDNA binding protein / OB-fold | ||||||
Function / homology | Function and homology information protein localization to chromosome / DNA replication factor A complex / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / regulation of DNA damage 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 ...protein localization to chromosome / DNA replication factor A complex / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / regulation of DNA damage 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 / regulation of double-strand break repair via homologous recombination / telomeric DNA binding / regulation of mitotic cell cycle / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / Activation of ATR in response to replication stress / mitotic G1 DNA damage checkpoint signaling / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / PML body / Meiotic recombination / 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 / regulation of cell population proliferation / Processing of DNA double-strand break ends / protein phosphatase binding / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / ubiquitin protein ligase binding / chromatin / enzyme binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Deng, X. / Borgstahl, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structure of the full-length human RPA14/32 complex gives insights into the mechanism of DNA binding and complex formation. Authors: Deng, X. / Habel, J.E. / Kabaleeswaran, V. / Snell, E.H. / Wold, M.S. / Borgstahl, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pqa.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pqa.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/2pqa ftp://data.pdbj.org/pub/pdb/validation_reports/pq/2pqa | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | RPA32 and RPA14 form a heterodimer |
-Components
#1: Protein | Mass: 14660.864 Da / Num. of mol.: 2 / Fragment: UNP residues 42-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPA2, REPA2, RPA32 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P15927 #2: Protein | Mass: 16117.456 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPA3, REPA3, RPA14 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P35244 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 57.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1 M Bicine pH 9, 20% saturated ammonium sulfate, 10% acetonitrile, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 9.0 |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9794728, 0.979609, 0.999879 | ||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 26, 2000 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→50 Å / Num. all: 25200 / Num. obs: 24160 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 49.6 Å2 / Rsym value: 0.098 / Net I/σ(I): 16.3 | ||||||||||||
Reflection shell | Resolution: 2.4→2.58 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 3730 / Rsym value: 0.58 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.884 / SU B: 10.578 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.551 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: High R value due to the disordered domain
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.724 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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