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- PDB-5eay: Crystal structure of a Dna2 peptide in complex with Rpa 70N -

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Basic information

Entry
Database: PDB / ID: 5eay
TitleCrystal structure of a Dna2 peptide in complex with Rpa 70N
Components
  • DNA replication ATP-dependent helicase/nuclease DNA2
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


: / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA replication, Okazaki fragment processing / protein localization to chromosome / nucleic acid metabolic process / : / DNA replication factor A complex ...: / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA replication, Okazaki fragment processing / protein localization to chromosome / nucleic acid metabolic process / : / DNA replication factor A complex / telomere maintenance via semi-conservative replication / t-circle formation / mitotic telomere maintenance via semi-conservative replication / mitochondrial DNA replication / nuclease activity / DNA clamp loader activity / 5'-flap endonuclease activity / DNA double-strand break processing / replication fork reversal / DNA replication checkpoint signaling / single-stranded telomeric DNA binding / lateral element / Impaired BRCA2 binding to PALB2 / DNA replication, removal of RNA primer / G-rich strand telomeric DNA binding / chromatin-protein adaptor activity / protein localization to site of double-strand break / 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 / single-stranded DNA helicase activity / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / mitochondrial DNA repair / Impaired BRCA2 binding to RAD51 / hemopoiesis / mitochondrial nucleoid / site of DNA damage / 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 / telomere maintenance via telomerase / mismatch repair / SUMOylation of DNA damage response and repair proteins / Activation of ATR in response to replication stress / homeostasis of number of cells within a tissue / telomere maintenance / DNA helicase activity / Translesion synthesis by REV1 / male germ cell nucleus / Translesion synthesis by POLK / positive regulation of DNA replication / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / helicase activity / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / G2/M DNA damage checkpoint / PML body / base-excision repair / Meiotic recombination / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / 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 / site of double-strand break / Processing of DNA double-strand break ends / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / DNA recombination / DNA helicase / Regulation of TP53 Activity through Phosphorylation / in utero embryonic development / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA replication / DNA repair / positive regulation of cell population proliferation / DNA damage response / chromatin binding / ATP hydrolysis activity / mitochondrion / DNA binding
Similarity search - Function
: / : / Dna2 Rift barrel domain / DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain ...: / : / Dna2 Rift barrel domain / DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / PD-(D/E)XK endonuclease-like domain superfamily / DNA2/NAM7 helicase, helicase domain / AAA domain / : / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit / DNA replication ATP-dependent helicase/nuclease DNA2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZhou, C. / Pourmal, S. / Pavletich, N.P.
CitationJournal: Elife / Year: 2015
Title: Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.
Authors: Zhou, C. / Pourmal, S. / Pavletich, N.P.
History
DepositionOct 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication protein A 70 kDa DNA-binding subunit
B: Replication protein A 70 kDa DNA-binding subunit
C: Replication protein A 70 kDa DNA-binding subunit
D: Replication protein A 70 kDa DNA-binding subunit
E: DNA replication ATP-dependent helicase/nuclease DNA2
F: DNA replication ATP-dependent helicase/nuclease DNA2
G: DNA replication ATP-dependent helicase/nuclease DNA2
H: DNA replication ATP-dependent helicase/nuclease DNA2


Theoretical massNumber of molelcules
Total (without water)58,5048
Polymers58,5048
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-40 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.303, 50.882, 76.528
Angle α, β, γ (deg.)90.000, 103.940, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Replication protein A 70 kDa DNA-binding subunit / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein


Mass: 12957.045 Da / Num. of mol.: 4 / Fragment: UNP residues 3-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Production host: Escherichia coli (E. coli) / References: UniProt: P27694
#2: Protein/peptide
DNA replication ATP-dependent helicase/nuclease DNA2 / hDNA2 / DNA replication ATP-dependent helicase-like homolog


Mass: 1668.884 Da / Num. of mol.: 4 / Fragment: UNP residues 1-17 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51530

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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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 50 mM Tris-HCl, 35 % PEG 1500, 2 mM TCEP, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→60 Å / Num. obs: 67556 / % possible obs: 84.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.051 / Rrim(I) all: 0.091 / Χ2: 1.961 / Net I/av σ(I): 23.455 / Net I/σ(I): 16.7 / Num. measured all: 184727
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.552.70.80163420.5250.5410.971.70679.7
1.55-1.622.80.58462550.6990.3860.7031.74178.6
1.62-1.692.80.44263000.8270.2880.5291.80779.1
1.69-1.782.80.29562930.9140.1930.3541.81679
1.78-1.892.80.1964060.9660.1250.2281.97880
1.89-2.042.70.11665520.9840.0770.142.10382
2.04-2.242.70.07869030.990.0530.0952.20686.1
2.24-2.562.60.06172790.9930.0420.0742.25990.8
2.56-3.232.60.04975040.9950.0350.0612.36393.3
3.23-602.80.03177220.9970.0220.0381.64593.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B29

2b29


Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.909 / SU B: 1.759 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2667 1815 3.1 %RANDOM
Rwork0.2316 ---
obs0.2327 57455 81.14 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 92.42 Å2 / Biso mean: 19.703 Å2 / Biso min: 5.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.19 Å2
2---0.09 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3933 0 0 0 3933
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193981
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9965375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47525.422166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29115765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5451524
X-RAY DIFFRACTIONr_chiral_restr0.0810.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212852
X-RAY DIFFRACTIONr_mcbond_it2.6242.7211996
X-RAY DIFFRACTIONr_mcangle_it4.0354.8252474
X-RAY DIFFRACTIONr_scbond_it3.9993.6221985
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 128 -
Rwork0.252 3649 -
all-3777 -
obs--69.94 %

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