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- PDB-6j8y: Crystal structure of the human RAD9-HUS1-RAD1-RHINO complex -

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Basic information

Entry
Database: PDB / ID: 6j8y
TitleCrystal structure of the human RAD9-HUS1-RAD1-RHINO 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 / exonuclease / hydrolase / nuclease / nucleus / phosphoprotein / pcna
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 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / : / Alpha Beta
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: 2.4 Å
AuthorsHara, K. / Iida, N. / Sakurai, H. / Hashimoto, H.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure of the RAD9-RAD1-HUS1 checkpoint clamp bound to RHINO sheds light on the other side of the DNA clamp.
Authors: Hara, K. / Iida, N. / Tamafune, R. / Ohashi, E. / Sakurai, H. / Ishikawa, Y. / Hishiki, A. / Hashimoto, H.
History
DepositionJan 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)96,3684
Polymers96,3684
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-30 kcal/mol
Surface area34710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.937, 136.190, 154.043
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 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: 31854.201 Da / Num. of mol.: 1
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: 2206.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHNO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BSD3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium citrate, Bis-tris propane pH 7.5

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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: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 44421 / % possible obs: 99.6 % / Redundancy: 6.68 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066176 / Net I/σ(I): 21.17
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.7791 / Num. unique obs: 27653 / CC1/2: 0.742

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A1J

3a1j


Resolution: 2.4→19.802 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.97
RfactorNum. reflection% reflection
Rfree0.2581 2248 5.06 %
Rwork0.2184 --
obs0.2205 44415 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 0 0 68 6268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036312
X-RAY DIFFRACTIONf_angle_d0.6988526
X-RAY DIFFRACTIONf_dihedral_angle_d14.5842335
X-RAY DIFFRACTIONf_chiral_restr0.026998
X-RAY DIFFRACTIONf_plane_restr0.0031083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3986-2.45060.33621290.28372557X-RAY DIFFRACTION99
2.4506-2.50750.38781220.30552620X-RAY DIFFRACTION100
2.5075-2.57010.34831370.29632603X-RAY DIFFRACTION100
2.5701-2.63950.35271500.29432600X-RAY DIFFRACTION100
2.6395-2.71690.35261410.2842580X-RAY DIFFRACTION100
2.7169-2.80440.32251470.27762616X-RAY DIFFRACTION100
2.8044-2.90430.34031400.28232600X-RAY DIFFRACTION100
2.9043-3.02020.33641280.27632626X-RAY DIFFRACTION100
3.0202-3.15720.28631480.26422604X-RAY DIFFRACTION100
3.1572-3.32290.28881350.24342658X-RAY DIFFRACTION100
3.3229-3.530.28661370.23062629X-RAY DIFFRACTION100
3.53-3.80080.25041410.21912645X-RAY DIFFRACTION100
3.8008-4.180.28851580.20162635X-RAY DIFFRACTION100
4.18-4.77740.18351500.15962659X-RAY DIFFRACTION100
4.7774-5.99130.23761390.18072714X-RAY DIFFRACTION100
5.9913-19.80280.18491460.18652821X-RAY DIFFRACTION100

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