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- PDB-2pi2: Full-length Replication protein A subunits RPA14 and RPA32 -

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Basic information

Entry
Database: PDB / ID: 2pi2
TitleFull-length Replication protein A subunits RPA14 and RPA32
Components
  • Replication protein A 14 kDa subunit
  • Replication protein A 32 kDa subunit
KeywordsREPLICATION / DNA BINDING PROTEIN / full-length RPA14/32 / ssDNA binding protein / OB-fold / Dioxane
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 / regulation of mitotic cell cycle / 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 / regulation of cell population proliferation / site of double-strand break / 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 / 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
1,4-DIETHYLENE DIOXIDE / Replication protein A 32 kDa subunit / Replication protein A 14 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionApr 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replication protein A 32 kDa subunit
B: Replication protein A 32 kDa subunit
C: Replication protein A 32 kDa subunit
D: Replication protein A 32 kDa subunit
E: Replication protein A 14 kDa subunit
F: Replication protein A 14 kDa subunit
G: Replication protein A 14 kDa subunit
H: Replication protein A 14 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,92912
Polymers181,5778
Non-polymers3524
Water4,396244
1
A: Replication protein A 32 kDa subunit
E: Replication protein A 14 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4823
Polymers45,3942
Non-polymers881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-13 kcal/mol
Surface area12220 Å2
MethodPISA, PQS
2
B: Replication protein A 32 kDa subunit
F: Replication protein A 14 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4823
Polymers45,3942
Non-polymers881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-13 kcal/mol
Surface area11970 Å2
MethodPISA, PQS
3
C: Replication protein A 32 kDa subunit
G: Replication protein A 14 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4823
Polymers45,3942
Non-polymers881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-15 kcal/mol
Surface area11930 Å2
MethodPISA, PQS
4
D: Replication protein A 32 kDa subunit
H: Replication protein A 14 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4823
Polymers45,3942
Non-polymers881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-13 kcal/mol
Surface area11710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.485, 139.826, 171.842
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
Replication protein A 32 kDa subunit / RP-A / RF-A / Replication factor-A protein 2 / p32 / p34


Mass: 29276.795 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA2, REPA2, RPA32 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P15927
#2: Protein
Replication protein A 14 kDa subunit / RP-A / RF-A / Replication factor-A protein 3 / p14


Mass: 16117.456 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA3, REPA3, RPA14 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P35244
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% dioxane, 0.1 M MES pH 6.5, 39% saturated ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 170250 / Num. obs: 162767 / % possible obs: 95 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 3.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.7 / % possible all: 98.59

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QUQ

1quq


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.585 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25487 6579 5 %RANDOM
Rwork0.23208 ---
obs0.23324 124950 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.137 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.78 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7612 0 24 244 7880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227779
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.96710537
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9245960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42124.8325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4761534
X-RAY DIFFRACTIONr_chiral_restr0.0980.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025692
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.23289
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25252
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2398
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.951.55019
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60827936
X-RAY DIFFRACTIONr_scbond_it1.73933089
X-RAY DIFFRACTIONr_scangle_it2.7814.52601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 491 -
Rwork0.297 9042 -
obs--98.59 %

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