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- PDB-2z6k: Crystal structure of full-length human RPA14/32 heterodimer -

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Basic information

Entry
Database: PDB / ID: 2z6k
TitleCrystal structure of full-length human RPA14/32 heterodimer
Components
  • Replication protein A 14 kDa subunit
  • Replication protein A 32 kDa subunit
KeywordsREPLICATION / full-length RPA14/32 / ssDNA binding protein / OB-fold / Acetylation / Alternative splicing / DNA replication / Nucleus / Phosphorylation / Polymorphism
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 / 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 / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / mitotic G1 DNA damage checkpoint signaling / telomere maintenance / regulation of mitotic cell cycle / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / nucleotide-excision repair / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / G2/M DNA damage checkpoint / PML body / base-excision repair / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Meiotic recombination / site of double-strand break / single-stranded DNA binding / regulation of cell population proliferation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / protein phosphatase binding / 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
Replication protein A 32 kDa subunit / Replication protein A 14 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDeng, X. / Habel, J.E. / Kabaleeswaran, V. / 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
DepositionAug 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Replication protein A 32 kDa subunit
C: Replication protein A 14 kDa subunit
D: Replication protein A 14 kDa subunit


Theoretical massNumber of molelcules
Total (without water)90,7894
Polymers90,7894
Non-polymers00
Water00
1
A: Replication protein A 32 kDa subunit
C: Replication protein A 14 kDa subunit


Theoretical massNumber of molelcules
Total (without water)45,3942
Polymers45,3942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
MethodPISA
2
B: Replication protein A 32 kDa subunit
D: Replication protein A 14 kDa subunit


Theoretical massNumber of molelcules
Total (without water)45,3942
Polymers45,3942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.460, 97.460, 125.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Replication protein A 32 kDa subunit / RPA32 / RP-A / RF-A / Replication factor-A protein 2 / p32 / p34


Mass: 29276.795 Da / Num. of mol.: 2 / Fragment: residues 42-175
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 / RPA14 / 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 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / 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: 3.286145 Å3/Da / Density % sol: 62.570122 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.9
Details: 0.95M KNa tartrate, 0.1M MES, 10mM DTT, pH 5.9, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 26620 / Num. obs: 25484 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 90 Å2 / Rsym value: 0.07 / Net I/σ(I): 16
Reflection shellResolution: 2.98→3.1 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2647 / Rsym value: 0.7 / % possible all: 99

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Processing

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

1quq


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.237 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.511 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1168 5 %RANDOM
Rwork0.22723 ---
obs0.22921 22594 99.91 %-
all-22616 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.456 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--1.54 Å20 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 0 0 3818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9645282
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2925482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.40724.788165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33415690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5511518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022864
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.21753
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22687
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2122
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.741.52477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33823982
X-RAY DIFFRACTIONr_scbond_it1.20331538
X-RAY DIFFRACTIONr_scangle_it2.1054.51300
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 102 -
Rwork0.328 1594 -
obs--100 %

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