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- PDB-7xuv: Crystal structure of RPA70N-RMI1 fusion -

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Basic information

Entry
Database: PDB / ID: 7xuv
TitleCrystal structure of RPA70N-RMI1 fusion
Components
  • RecQ-mediated genome instability protein 1
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsDNA BINDING PROTEIN / RPA / RPA70N / RMI1
Function / homology
Function and homology information


RecQ family helicase-topoisomerase III complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / protein localization to chromosome / DNA replication factor A complex / resolution of meiotic recombination intermediates / lateral element / Impaired BRCA2 binding to PALB2 / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding ...RecQ family helicase-topoisomerase III complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / protein localization to chromosome / DNA replication factor A complex / resolution of meiotic recombination intermediates / lateral element / Impaired BRCA2 binding to PALB2 / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / 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 / 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) / Impaired BRCA2 binding to RAD51 / hemopoiesis / Presynaptic phase of homologous DNA pairing and strand exchange / site of DNA damage / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / HSF1 activation / response to glucose / telomere maintenance via telomerase / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / homeostasis of number of cells within a tissue / 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 / male germ cell nucleus / nucleotide-excision repair / 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 / base-excision repair / PML body / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Meiotic recombination / DNA-templated DNA replication / multicellular organism growth / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / glucose homeostasis / single-stranded DNA binding / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / in utero embryonic development / damaged DNA binding / chromosome, telomeric region / DNA replication / nuclear body / DNA repair / nucleotide binding / positive regulation of cell population proliferation / DNA damage response / chromatin binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
RecQ-mediated genome instability protein 1, C-terminal OB-fold domain / RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily / : / Recq-mediated genome instability protein 1, C-terminal OB-fold / RMI1, N-terminal helical domain / DUF1767 / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / Replication factor-A protein 1, N-terminal domain ...RecQ-mediated genome instability protein 1, C-terminal OB-fold domain / RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily / : / Recq-mediated genome instability protein 1, C-terminal OB-fold / RMI1, N-terminal helical domain / DUF1767 / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold 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 / : / 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 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit / RecQ-mediated genome instability protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWu, Y.Y. / Zang, N. / Fu, W.M. / Zhou, C.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, China) 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
DepositionMay 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3May 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: RecQ-mediated genome instability protein 1


Theoretical massNumber of molelcules
Total (without water)15,5392
Polymers15,5392
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-3 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.930, 50.263, 52.308
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 13187.371 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 RecQ-mediated genome instability protein 1 / BLM-associated protein of 75 kDa / BLAP75 / FAAP75


Mass: 2351.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RMI1, C9orf76 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9A7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.73 Å3/Da / Density % sol: 28.96 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 30% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.6→36.24 Å / Num. obs: 22637 / % possible obs: 89.41 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.0317 / Net I/σ(I): 13.8
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.342 / Num. unique obs: 2779 / CC1/2: 0.953 / Rpim(I) all: 0.1578

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EAY

5eay


Resolution: 1.6→36.24 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 1176 5.2 %
Rwork0.1866 21461 -
obs0.1884 22637 82.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.82 Å2 / Biso mean: 21.2182 Å2 / Biso min: 9.76 Å2
Refinement stepCycle: final / Resolution: 1.6→36.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 0 0 107 1123
Biso mean---29.32 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.670.25131760.22432779295586
1.67-1.760.24791340.21272759289385
1.76-1.870.28481220.20382784290684
1.87-2.020.23831370.18922747288484
2.02-2.220.19421710.18252648281983
2.22-2.540.23341300.19052664279481
2.54-3.20.22751660.19862563272979
3.2-36.240.19551400.16382517265777
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)
12.6574-0.4168-0.56034.21630.07342.3760.03690.08860.0996-0.2139-0.0070.0077-0.0922-0.0820.02350.1162-0.0091-0.0050.1258-0.00530.08021.5769-2.1442-14.3822
22.2007-0.5906-0.6990.3268-0.55843.46210.0152-0.16190.0171-0.00740.1375-0.1246-0.25250.4832-0.06480.0896-0.0153-0.02130.1253-0.00570.13165.728-2.1099-0.2604
37.12342.5933-2.46462.8107-3.37915.6850.2262-0.29520.40570.3907-0.12660.3187-0.6851-0.2478-0.11830.1626-0.0001-0.00940.127-0.00220.12951.19033.61113.5841
43.37110.7014-2.1712.9265-1.04143.33660.08870.0110.17360.101-0.00930.1354-0.0571-0.1012-0.07120.078-0.0096-0.02890.1018-0.00580.09020.2832-0.2219-0.6061
58.07981.0394-5.50172.608-1.27346.87170.1616-0.6279-0.32710.1739-0.25250.15480.08270.16670.05610.1827-0.0223-0.01590.18470.02710.16713.2585-8.99994.7854
61.1059-0.27680.27166.7007-1.77482.02960.04270.00760.07720.2565-0.03350.4049-0.1263-0.0005-0.0280.1165-0.00150.01790.130.00840.109-3.23574.7739-7.7132
71.6913-0.01410.13853.8304-0.11331.8837-0.0057-0.1063-0.12240.38890.02550.08710.1799-0.01770.01620.1403-0.0197-0.0040.10580.00750.066-0.8532-5.8351-2.9621
84.0352-0.54130.34833.9052-0.90135.00510.20180.09630.42390.3768-0.1402-0.893-0.38370.5401-0.04510.1201-0.0221-0.01150.23740.01510.257113.3552-1.9491-8.2235
92.41681.796-0.01368.87791.30833.37680.39940.40560.28460.2045-0.06810.3938-0.8449-0.2276-0.11510.50290.08810.04450.2330.02520.21460.4213.29950.3576
105.35380.5758-0.06020.387-0.30460.317-0.5063-1.22350.17660.48850.2883-0.14810.14230.57830.2010.43530.1230.04930.3577-0.01660.2905-7.1820.1409-1.8126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 23 )A1 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 32 )A24 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 47 )A33 - 47
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 67 )A48 - 67
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 75 )A68 - 75
6X-RAY DIFFRACTION6chain 'A' and (resid 76 through 91 )A76 - 91
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 108 )A92 - 108
8X-RAY DIFFRACTION8chain 'A' and (resid 109 through 118 )A109 - 118
9X-RAY DIFFRACTION9chain 'B' and (resid 7 through 251 )B7 - 251
10X-RAY DIFFRACTION10chain 'B' and (resid 252 through 259 )B252 - 259

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