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- PDB-1quq: COMPLEX OF REPLICATION PROTEIN A SUBUNITS RPA14 AND RPA32 -

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Basic information

Entry
Database: PDB / ID: 1quq
TitleCOMPLEX OF REPLICATION PROTEIN A SUBUNITS RPA14 AND RPA32
Components
  • PROTEIN (REPLICATION PROTEIN A 14 KD SUBUNIT)
  • PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT)
KeywordsDNA BINDING PROTEIN / RPA / OB-FOLD / SSDNA-BINDING / DNA-BINDING PROTEIN
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / regulation of DNA damage checkpoint / 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 / G-rich strand telomeric DNA binding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 ...protein localization to chromosome / DNA replication factor A complex / regulation of DNA damage checkpoint / 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 / G-rich strand telomeric DNA binding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / regulation of double-strand break repair via homologous recombination / telomeric DNA binding / Presynaptic phase of homologous DNA pairing and strand exchange / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / 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 / regulation of mitotic cell cycle / 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 / Recognition of DNA damage by PCNA-containing replication complex / 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 / site of double-strand break / single-stranded DNA binding / regulation of cell population proliferation / Processing of DNA double-strand break ends / protein phosphatase binding / DNA replication / Regulation of TP53 Activity through Phosphorylation / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA repair / 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 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 / Winged helix-like DNA-binding domain superfamily ...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 / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / 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 / MAD / Resolution: 2.5 Å
AuthorsBochkarev, A. / Bochkareva, E. / Frappier, L. / Edwards, A.M.
Citation
Journal: EMBO J. / Year: 1999
Title: The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding.
Authors: Bochkarev, A. / Bochkareva, E. / Frappier, L. / Edwards, A.M.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: The Rpa32 Subunit of Human Replication Protein a Contains a Single-Stranded DNA-Binding Domain.
Authors: Bochkareva, E. / Frappier, L. / Edwards, A.M. / Bochkarev, A.
History
DepositionJul 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Structure summary / Category: software / struct_keywords / Item: _struct_keywords.text
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT)
B: PROTEIN (REPLICATION PROTEIN A 14 KD SUBUNIT)
C: PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT)
D: PROTEIN (REPLICATION PROTEIN A 14 KD SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)56,0334
Polymers56,0334
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT)
D: PROTEIN (REPLICATION PROTEIN A 14 KD SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)28,0162
Polymers28,0162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-17 kcal/mol
Surface area11490 Å2
MethodPISA, PQS
3
A: PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT)
B: PROTEIN (REPLICATION PROTEIN A 14 KD SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)28,0162
Polymers28,0162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-17 kcal/mol
Surface area11430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.700, 76.600, 119.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT)


Mass: 14432.592 Da / Num. of mol.: 2 / Fragment: CENTRAL DOMAIN, RESIDUES 43-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Plasmid: PET15B / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P15927
#2: Protein PROTEIN (REPLICATION PROTEIN A 14 KD SUBUNIT)


Mass: 13583.714 Da / Num. of mol.: 2 / Fragment: RPA14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Plasmid: PET15B / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P35244
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Description: MAD EXPERIMENT WAS COLLECTED AT CHESS BEAMLINE F2 IN APRIL 1998. DETECTOR - ADSC Q4. SOFTWARE - DENZO, SCALEPACK
Crystal growpH: 6.5
Details: 0.1 M MES, 0.75 M AMMONIUM SULPHATE, 20% PEG 8K, 10 MM DTT., pH 6.50
Temp details: 8
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MMES1reservoir
20.75 Mammonium sulfate1reservoir
320 %PEG80001reservoir
410 mMdithiothreitol1reservoir
515 mg/mlprotain1drop
61 mMHEPES1drop
750 mM1dropNaCl
810 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 1, 1998 / Details: OSMIC MULTILAYER
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 23882 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 34.4
Reflection shellResolution: 2.4→2.49 Å / Rsym value: 16.2 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Num. measured all: 123441
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 7

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Processing

Software
NameVersionClassification
SnBphasing
PHASESphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: USED RESOLUTION DEPENDENT WEIGHTING AND BULK SOLVENT MODEL CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2045 10 %RANDOM
Rwork0.212 ---
obs0.212 20990 97.8 %-
Displacement parametersBiso mean: 22.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3669 0 0 117 3786
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.354 229 8.7 %
Rwork0.202 2280 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOP.H2O
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / % reflection Rfree: 8.7 % / Rfactor Rwork: 0.202

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