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- PDB-8k00: RPA70N-MRE11 fusion -

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Basic information

Entry
Database: PDB / ID: 8k00
TitleRPA70N-MRE11 fusion
Components
  • Double-strand break repair protein MRE11
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsDNA BINDING PROTEIN / RPA / 70N / MRE11
Function / homology
Function and homology information


chromosomal region / telomeric 3' overhang formation / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / negative regulation of double-strand break repair via nonhomologous end joining / protein localization to chromosome / meiotic DNA double-strand break formation / Sensing of DNA Double Strand Breaks / BRCA1-C complex / regulation of mitotic recombination ...chromosomal region / telomeric 3' overhang formation / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / negative regulation of double-strand break repair via nonhomologous end joining / protein localization to chromosome / meiotic DNA double-strand break formation / Sensing of DNA Double Strand Breaks / BRCA1-C complex / regulation of mitotic recombination / DNA replication factor A complex / R-loop processing / chromatin-protein adaptor activity / homologous chromosome pairing at meiosis / DNA strand resection involved in replication fork processing / DNA double-strand break processing / nuclease activity / single-stranded DNA endodeoxyribonuclease activity / homologous recombination / positive regulation of telomere maintenance / Removal of the Flap Intermediate / Cytosolic sensors of pathogen-associated DNA / single-stranded telomeric DNA binding / protein localization to site of double-strand break / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Impaired BRCA2 binding to PALB2 / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / HDR through MMEJ (alt-NHEJ) / G-rich strand telomeric DNA binding / IRF3-mediated induction of type I IFN / mitotic G2/M transition checkpoint / positive regulation of kinase activity / reciprocal meiotic recombination / sister chromatid cohesion / mitotic intra-S DNA damage checkpoint signaling / 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 / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / 3'-5'-DNA exonuclease activity / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / 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 / SUMOylation of DNA damage response and repair proteins / positive regulation of protein autophosphorylation / 3'-5' exonuclease activity / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / DNA endonuclease activity / replication fork / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / Nonhomologous End-Joining (NHEJ) / 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 / DNA Damage/Telomere Stress Induced Senescence / DNA-templated DNA replication / PML body / Meiotic recombination / Formation of Incision Complex in GG-NER / double-strand break repair via nonhomologous end joining / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / single-stranded DNA binding / manganese ion binding / Processing of DNA double-strand break ends / double-stranded DNA binding / DNA recombination / DNA replication / Regulation of TP53 Activity through Phosphorylation / cell population proliferation / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds
Similarity search - Function
DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / 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 ...DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / 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 / Mre11 nuclease, N-terminal metallophosphatase domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit / Double-strand break repair protein MRE11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFu, W.M. / Wu, Y.Y. / Zhou, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Elife / Year: 2023
Title: Structural characterization of human RPA70N association with DNA damage response proteins.
Authors: Wu, Y. / Fu, W. / Zang, N. / Zhou, C.
History
DepositionJul 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.pdbx_database_id_DOI ..._citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

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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: Double-strand break repair protein MRE11


Theoretical massNumber of molelcules
Total (without water)16,4132
Polymers16,4132
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-3 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.900, 53.705, 55.329
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 70 kDa DNA-binding subunit / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein


Mass: 13274.449 Da / Num. of mol.: 1
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 Double-strand break repair protein MRE11 / Double-strand break repair protein MRE11A / Meiotic recombination 11 homolog 1 / MRE11 homolog 1 / ...Double-strand break repair protein MRE11A / Meiotic recombination 11 homolog 1 / MRE11 homolog 1 / Meiotic recombination 11 homolog A / MRE11 homolog A


Mass: 3138.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRE11, HNGS1, MRE11A / Production host: Escherichia coli (E. coli)
References: UniProt: P49959, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 1.77 Å3/Da / Density % sol: 30.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.4→27.38 Å / Num. obs: 44033 / % possible obs: 99.82 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.0582 / Net I/σ(I): 23.61
Reflection shellResolution: 1.4→1.43 Å / Rmerge(I) obs: 0.08074 / Num. unique obs: 2576 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4924: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XV4

7xv4


Resolution: 1.4→27.38 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 2285 5.19 %
Rwork0.1731 --
obs0.1744 44033 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→27.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 0 195 1327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.745
X-RAY DIFFRACTIONf_dihedral_angle_d14.537440
X-RAY DIFFRACTIONf_chiral_restr0.077190
X-RAY DIFFRACTIONf_plane_restr0.005205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.23781570.20622576X-RAY DIFFRACTION99
1.43-1.460.21241090.19532644X-RAY DIFFRACTION100
1.46-1.50.21911200.1922655X-RAY DIFFRACTION100
1.5-1.540.24571510.1822627X-RAY DIFFRACTION100
1.54-1.590.2251360.17842581X-RAY DIFFRACTION100
1.59-1.640.22071370.17282598X-RAY DIFFRACTION100
1.64-1.70.22681900.17962574X-RAY DIFFRACTION100
1.7-1.760.17861160.18962645X-RAY DIFFRACTION100
1.76-1.840.22961440.17652627X-RAY DIFFRACTION100
1.84-1.940.2141340.15862593X-RAY DIFFRACTION100
1.94-2.060.15021570.15792605X-RAY DIFFRACTION100
2.06-2.220.19391880.15932553X-RAY DIFFRACTION100
2.22-2.450.15541400.16322625X-RAY DIFFRACTION100
2.45-2.80.22661200.18272643X-RAY DIFFRACTION100
2.8-3.520.18641520.1732589X-RAY DIFFRACTION100
3.53-27.380.19311340.16992613X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4097-3.644-2.71213.08492.21052.31010.37460.28730.2987-0.3077-0.1813-0.3556-0.32620.1939-0.15410.08170.0030.03410.09140.01230.0912-1.79450.3017-0.1346
22.9458-0.371.52452.25691.89014.9356-0.0754-0.30770.3050.0988-0.07290.1822-0.2799-0.41390.02370.09060.00990.02450.0813-0.00760.076-11.32813.393912.1128
31.26971.0917-1.76811.7881-1.2972.6108-0.0922-0.2065-0.2410.0374-0.1094-0.23530.1820.17440.15730.05580.0104-0.00050.05670.01870.0766-3.0084-12.165910.5958
40.16150.64110.21563.37160.38210.54370.255-1.6496-1.27871.3346-0.09760.40230.563-0.674-0.09020.3416-0.03370.00830.41780.19710.3598-11.7151-23.581422.8215
54.31555.2123-3.31946.6601-4.08332.55690.0583-0.1001-0.10230.0425-0.0723-0.06560.07380.05530.01160.0855-0.0084-0.0060.07810.01570.0703-5.5441-12.026314.1914
62.41622.3155-0.48083.6666-0.10631.19780.1119-0.05470.04880.1548-0.05540.15140.0229-0.0258-0.04250.04820.0162-0.01870.04690.00420.0582-8.33-10.990611.96
77.5175.7896-2.08584.5393-1.94492.29310.07510.0188-0.3364-0.0337-0.063-0.17850.17110.0266-0.03520.08830.0126-0.00440.0813-0.0170.1031-5.6741-17.74063.9385
80.1816-0.12920.42650.48590.81553.87280.029-0.0471-0.0180.04770.0149-0.03890.0516-0.2012-0.0590.0441-0.0021-0.00620.0508-0.00750.0571-12.5188-5.16115.7654
91.6923-0.7118-1.34441.04941.40395.13640.01370.1175-0.1291-0.05290.0105-0.059-0.0833-0.1102-0.02860.0543-0.01260.00380.0321-0.0050.0557-12.4957-8.08149.3367
102.10970.11710.1661.47321.38264.26830.07330.0606-0.113-0.0918-0.0686-0.0293-0.10950.1638-0.07120.04040.0067-0.00110.049-0.00670.07422.1166-6.3285.3934
110.0092-0.00160.04290.0125-0.06080.1730.47770.02610.569-0.3426-0.2019-0.0175-0.49390.0457-0.30720.26740.00850.07740.1830.03270.31380.6652-9.990123.3648
128.6233-2.20884.46662.4948-1.48663.62680.1256-0.0699-0.1606-0.1320.00930.26480.0277-0.2433-0.18630.13230.00040.02160.14420.00120.1611-21.3506-11.226521.3308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 23 )
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 33 )
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 40 )
5X-RAY DIFFRACTION5chain 'A' and (resid 41 through 47 )
6X-RAY DIFFRACTION6chain 'A' and (resid 48 through 67 )
7X-RAY DIFFRACTION7chain 'A' and (resid 68 through 75 )
8X-RAY DIFFRACTION8chain 'A' and (resid 76 through 91 )
9X-RAY DIFFRACTION9chain 'A' and (resid 92 through 103 )
10X-RAY DIFFRACTION10chain 'A' and (resid 104 through 119 )
11X-RAY DIFFRACTION11chain 'B' and (resid 533 through 541 )
12X-RAY DIFFRACTION12chain 'B' and (resid 542 through 563 )

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