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- PDB-4ou0: Crystal Structure of RPA32C -

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Basic information

Entry
Database: PDB / ID: 4ou0
TitleCrystal Structure of RPA32C
ComponentsReplication protein A 32 kDa subunit
KeywordsDNA BINDING PROTEIN / winged-helix turn helix / protein-protein interaction / S-Methyl-Thio-Cysteine
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / regulation of DNA damage checkpoint / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / HDR through Single Strand Annealing (SSA) / regulation of double-strand break repair via homologous recombination ...protein localization to chromosome / DNA replication factor A complex / regulation of DNA damage checkpoint / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / HDR through Single Strand Annealing (SSA) / regulation of double-strand break repair via homologous recombination / Impaired BRCA2 binding to RAD51 / telomeric DNA binding / 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 / mismatch repair / 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 / 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 / G2/M DNA damage checkpoint / base-excision repair / PML body / Meiotic recombination / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / 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 / Processing of DNA double-strand break ends / protein phosphatase binding / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / chromosome, telomeric region / DNA replication / nuclear body / ubiquitin protein ligase binding / chromatin / enzyme binding / nucleoplasm / nucleus
Similarity search - Function
Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Replication protein A 32 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFeldkamp, M.D. / Mason, A.C. / Eichman, B.F. / Chazin, W.J.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Analysis of Replication Protein A Recruitment of the DNA Damage Response Protein SMARCAL1.
Authors: Feldkamp, M.D. / Mason, A.C. / Eichman, B.F. / Chazin, W.J.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Dec 9, 2015Group: Structure summary
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication protein A 32 kDa subunit


Theoretical massNumber of molelcules
Total (without water)7,9961
Polymers7,9961
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.556, 69.556, 23.567
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Replication protein A 32 kDa subunit / RP-A p32 / Replication factor A protein 2 / RF-A protein 2 / Replication protein A 34 kDa subunit / RP-A p34


Mass: 7995.881 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 202-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REPA2, RFA2, RPA2, RPA32, RPA34 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 DE3 / References: UniProt: P15927
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 50 mM Sodium Acetate, 20% PEG 3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 12921 / % possible obs: 98.41 % / Redundancy: 7.6 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.46
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 4.51 / Num. unique all: 1161 / % possible all: 89.03

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.4_1496)model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DPU

1dpu


Resolution: 1.4→30 Å / SU ML: 0.12 / σ(F): 1.38 / Phase error: 30.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 630 4.88 %Random
Rwork0.1969 ---
obs0.1988 12910 98.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms503 0 0 53 556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003540
X-RAY DIFFRACTIONf_angle_d0.804733
X-RAY DIFFRACTIONf_dihedral_angle_d12.326196
X-RAY DIFFRACTIONf_chiral_restr0.04382
X-RAY DIFFRACTIONf_plane_restr0.00398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.54060.27821660.22152890X-RAY DIFFRACTION94
1.5406-1.76350.20751500.19183090X-RAY DIFFRACTION100
1.7635-2.22170.22641610.20153119X-RAY DIFFRACTION100
2.2217-30.12560.24331530.19413181X-RAY DIFFRACTION99

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