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- PDB-2pqa: Crystal Structure of Full-length Human RPA 14/32 Heterodimer -

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Basic information

Entry
Database: PDB / ID: 2pqa
TitleCrystal Structure of Full-length Human RPA 14/32 Heterodimer
Components
  • Replication protein A 14 kDa subunitDNA replication
  • Replication protein A 32 kDa subunitDNA replication
KeywordsREPLICATION / RPA14/32 / ssDNA binding protein / OB-fold
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 / 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) / 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 / 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) / regulation of double-strand break repair via homologous recombination / regulation of mitotic cell cycle / Presynaptic phase of homologous DNA pairing and strand exchange / mismatch repair / Regulation of HSF1-mediated heat shock response / HSF1 activation / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / telomere maintenance / mitotic G1 DNA damage checkpoint signaling / Translesion synthesis by REV1 / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by POLI / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / base-excision repair / Fanconi Anemia Pathway / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / G2/M DNA damage checkpoint / PML body / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Meiotic recombination / 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 / chromosome, telomeric region / protein N-terminus binding / protein phosphatase binding / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / nuclear body / chromatin / ubiquitin protein ligase binding / 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 3 / Replication factor A protein 3 / Replication factor A protein-like / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Nucleic acid-binding, OB-fold ...Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein 3 / Replication factor A protein 3 / Replication factor A protein-like / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Winged helix-like DNA-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication protein A 32 kDa subunit / Replication protein A 14 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsDeng, X. / Borgstahl, G.E.
CitationJournal: 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
DepositionMay 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication protein A 32 kDa subunit
B: Replication protein A 14 kDa subunit
C: Replication protein A 32 kDa subunit
D: Replication protein A 14 kDa subunit


Theoretical massNumber of molelcules
Total (without water)61,5574
Polymers61,5574
Non-polymers00
Water0
1
A: Replication protein A 32 kDa subunit
B: Replication protein A 14 kDa subunit


Theoretical massNumber of molelcules
Total (without water)30,7782
Polymers30,7782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-15 kcal/mol
Surface area12870 Å2
MethodPISA, PQS
2
C: Replication protein A 32 kDa subunit
D: Replication protein A 14 kDa subunit


Theoretical massNumber of molelcules
Total (without water)30,7782
Polymers30,7782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-19 kcal/mol
Surface area12450 Å2
MethodPISA, PQS
Unit cell
γ
α
β
Length a, b, c (Å)63.377, 63.377, 272.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsRPA32 and RPA14 form a heterodimer

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Components

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


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 Replication protein A 14 kDa subunit / DNA replication / RP-A / RF-A / Replication factor-A protein 3 / p14


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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 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

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9794728, 0.979609, 0.999879
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 26, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97947281
20.9796091
30.9998791
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.27981 1049 5.1 %RANDOM
Rwork0.22825 ---
obs0.23091 19411 96.03 %-
all-20156 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.724 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.84 Å20 Å2
2--1.69 Å20 Å2
3----2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3785 0 0 0 3785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223850
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9655220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5345477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37424.847163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50315687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5831517
X-RAY DIFFRACTIONr_chiral_restr0.1130.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022831
X-RAY DIFFRACTIONr_nbd_refined0.230.21580
X-RAY DIFFRACTIONr_nbtor_refined0.310.22595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.26
X-RAY DIFFRACTIONr_mcbond_it0.711.52472
X-RAY DIFFRACTIONr_mcangle_it1.23823938
X-RAY DIFFRACTIONr_scbond_it1.44731526
X-RAY DIFFRACTIONr_scangle_it2.2914.51282
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 76 -
Rwork0.31 1428 -
obs-1525 97.22 %

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