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- PDB-8wu8: Crystal structure of the human RAD9-RAD1(F64A/M256A/F266A)-HUS1-R... -

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Basic information

Entry
Database: PDB / ID: 8wu8
TitleCrystal structure of the human RAD9-RAD1(F64A/M256A/F266A)-HUS1-RHINO(88-99) complex
Components
  • Cell cycle checkpoint control protein RAD9A
  • Cell cycle checkpoint protein RAD1
  • Checkpoint protein HUS1
  • RAD9, HUS1, RAD1-interacting nuclear orphan protein 1
KeywordsCELL CYCLE / dna damage / checkpoint / dna repair / dna binding clamp
Function / homology
Function and homology information


meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / positive regulation of G0 to G1 transition / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mitotic DNA replication checkpoint signaling / recombinational repair ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / positive regulation of G0 to G1 transition / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mitotic DNA replication checkpoint signaling / recombinational repair / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / Activation of ATR in response to replication stress / response to UV / substantia nigra development / 3'-5' exonuclease activity / telomere maintenance / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / cellular response to ionizing radiation / nucleotide-excision repair / regulation of protein phosphorylation / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / histone deacetylase binding / SH3 domain binding / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / chromosome / site of double-strand break / Processing of DNA double-strand break ends / DNA replication / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / cell cycle / intracellular membrane-bounded organelle / DNA repair / DNA damage response / nucleolus / protein kinase binding / enzyme binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Rad9, Rad1, Hus1-interacting nuclear orphan protein 1 / RAD9, RAD1, HUS1-interacting nuclear orphan protein / Cell cycle checkpoint protein, Rad1 / Cell cycle checkpoint, Hus1 / Rad9 / Rad9 / Checkpoint protein Hus1/Mec3 / Hus1-like protein / Rad1/Rec1/Rad17 / Rad9/Ddc1 ...Rad9, Rad1, Hus1-interacting nuclear orphan protein 1 / RAD9, RAD1, HUS1-interacting nuclear orphan protein / Cell cycle checkpoint protein, Rad1 / Cell cycle checkpoint, Hus1 / Rad9 / Rad9 / Checkpoint protein Hus1/Mec3 / Hus1-like protein / Rad1/Rec1/Rad17 / Rad9/Ddc1 / Repair protein Rad1/Rec1/Rad17 / :
Similarity search - Domain/homology
Cell cycle checkpoint protein RAD1 / Checkpoint protein HUS1 / Cell cycle checkpoint control protein RAD9A / RAD9, HUS1, RAD1-interacting nuclear orphan protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsHara, K. / Nagata, K. / Iida, N. / Hashimoto, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural basis for intra- and intermolecular interactions on RAD9 subunit of 9-1-1 checkpoint clamp implies functional 9-1-1 regulation by RHINO.
Authors: Hara, K. / Tatsukawa, K. / Nagata, K. / Iida, N. / Hishiki, A. / Ohashi, E. / Hashimoto, H.
History
DepositionOct 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell cycle checkpoint control protein RAD9A
B: Checkpoint protein HUS1
C: Cell cycle checkpoint protein RAD1
D: RAD9, HUS1, RAD1-interacting nuclear orphan protein 1


Theoretical massNumber of molelcules
Total (without water)95,3424
Polymers95,3424
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-34 kcal/mol
Surface area35990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.115, 69.938, 83.948
Angle α, β, γ (deg.)90.00, 97.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell cycle checkpoint control protein RAD9A / hRAD9 / DNA repair exonuclease rad9 homolog A


Mass: 29746.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD9A / Production host: Escherichia coli (E. coli) / References: UniProt: Q99638, exodeoxyribonuclease III
#2: Protein Checkpoint protein HUS1 / hHUS1


Mass: 32560.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUS1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60921
#3: Protein Cell cycle checkpoint protein RAD1 / hRAD1 / DNA repair exonuclease rad1 homolog / Rad1-like DNA damage checkpoint protein


Mass: 31641.896 Da / Num. of mol.: 1 / Mutation: F64A, M256A, F266A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD1, REC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60671, exodeoxyribonuclease III
#4: Protein/peptide RAD9, HUS1, RAD1-interacting nuclear orphan protein 1 / RAD9 / RAD1 / HUS1-interacting nuclear orphan protein


Mass: 1392.554 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHNO1, C12orf32, RHINO, HKMT1188 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BSD3

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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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Potassium iodine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.81→35.771 Å / Num. obs: 19831 / % possible obs: 98.54 % / Redundancy: 3.4 % / CC1/2: 0.997 / Net I/σ(I): 15.87
Reflection shellResolution: 2.81→2.911 Å / Num. unique obs: 1984 / CC1/2: 0.659

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→35.771 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2669 1982 10 %
Rwork0.2148 --
obs0.2202 19825 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→35.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6171 0 0 0 6171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126280
X-RAY DIFFRACTIONf_angle_d0.88479
X-RAY DIFFRACTIONf_dihedral_angle_d12.8842329
X-RAY DIFFRACTIONf_chiral_restr0.035994
X-RAY DIFFRACTIONf_plane_restr0.0031077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8103-2.88050.3461420.30341281X-RAY DIFFRACTION100
2.8805-2.95840.3821420.29291276X-RAY DIFFRACTION100
2.9584-3.04540.4241420.29411274X-RAY DIFFRACTION99
3.0454-3.14360.33461410.26621269X-RAY DIFFRACTION100
3.1436-3.25590.30571430.24351284X-RAY DIFFRACTION100
3.2559-3.38620.31591410.2551276X-RAY DIFFRACTION99
3.3862-3.54020.27051400.23821264X-RAY DIFFRACTION97
3.5402-3.72660.29121390.24041248X-RAY DIFFRACTION99
3.7266-3.95980.34131440.22751295X-RAY DIFFRACTION99
3.9598-4.26510.28641410.22251270X-RAY DIFFRACTION99
4.2651-4.69350.21841420.17891276X-RAY DIFFRACTION98
4.6935-5.37070.21271400.1831256X-RAY DIFFRACTION98
5.3707-6.7590.29481420.22731275X-RAY DIFFRACTION97
6.759-35.7710.19651430.16741299X-RAY DIFFRACTION96

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