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- PDB-8gnn: Crystal structure of the human RAD9-RAD1-HUS1-RAD17 complex -

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Basic information

Entry
Database: PDB / ID: 8gnn
TitleCrystal structure of the human RAD9-RAD1-HUS1-RAD17 complex
Components
  • Cell cycle checkpoint control protein RAD9A
  • Cell cycle checkpoint protein RAD1
  • Cell cycle checkpoint protein RAD17
  • Checkpoint protein HUS1
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 / Rad17 RFC-like complex / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA clamp loader activity / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / regulation of phosphorylation ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / Rad17 RFC-like complex / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA clamp loader activity / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / regulation of phosphorylation / mitotic DNA replication checkpoint signaling / 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 / negative regulation of DNA replication / 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 / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / chromosome / site of double-strand break / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / intracellular membrane-bounded organelle / DNA repair / DNA damage response / chromatin binding / nucleolus / protein kinase binding / enzyme binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cell cycle checkpoint protein, Rad1 / Cell cycle checkpoint, Hus1 / Rad9 / Rad9 / Checkpoint protein Hus1/Mec3 / Hus1-like protein / Checkpoint protein Rad17/Rad24 / Checkpoint protein Rad17/Rad24, fungi/metazoa / Rad1/Rec1/Rad17 / Rad9/Ddc1 ...Cell cycle checkpoint protein, Rad1 / Cell cycle checkpoint, Hus1 / Rad9 / Rad9 / Checkpoint protein Hus1/Mec3 / Hus1-like protein / Checkpoint protein Rad17/Rad24 / Checkpoint protein Rad17/Rad24, fungi/metazoa / Rad1/Rec1/Rad17 / Rad9/Ddc1 / Repair protein Rad1/Rec1/Rad17 / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cell cycle checkpoint protein RAD1 / Checkpoint protein HUS1 / Cell cycle checkpoint protein RAD17 / Cell cycle checkpoint control protein RAD9A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.119 Å
AuthorsHara, K. / Nagata, K. / Iida, N. / Hashimoto, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The 9-1-1 DNA clamp subunit RAD1 forms specific interactions with clamp loader RAD17, revealing functional implications for binding-protein RHINO.
Authors: Hara, K. / Hishiki, A. / Hoshino, T. / Nagata, K. / Iida, N. / Sawada, Y. / Ohashi, E. / Hashimoto, H.
History
DepositionAug 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Cell cycle checkpoint protein RAD17


Theoretical massNumber of molelcules
Total (without water)95,5054
Polymers95,5054
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-25 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.188, 136.303, 154.046
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 Cell cycle checkpoint protein RAD17 / hRad17 / RF-C/activator 1 homolog


Mass: 1343.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75943
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Bis-Tris propane pH 7.5, sodium citrate, PEG 3350

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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: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.119→20 Å / Num. obs: 64368 / % possible obs: 99.86 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06731 / Rrim(I) all: 0.07296 / Net I/σ(I): 18.26
Reflection shellResolution: 2.119→2.24 Å / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 6285 / CC1/2: 0.761 / Rrim(I) all: 0.887 / % possible all: 99.56

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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: 6j8y

6j8y


Resolution: 2.119→19.806 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 2000 3.11 %
Rwork0.2174 --
obs0.2188 64362 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.119→19.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6294 0 0 252 6546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036409
X-RAY DIFFRACTIONf_angle_d0.6668658
X-RAY DIFFRACTIONf_dihedral_angle_d13.5432373
X-RAY DIFFRACTIONf_chiral_restr0.0281007
X-RAY DIFFRACTIONf_plane_restr0.0031106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1191-2.1720.36931380.3094320X-RAY DIFFRACTION99
2.172-2.23070.32291420.28924415X-RAY DIFFRACTION100
2.2307-2.29620.34921410.27584411X-RAY DIFFRACTION100
2.2962-2.37020.31551410.27414394X-RAY DIFFRACTION100
2.3702-2.45480.30051420.27374387X-RAY DIFFRACTION100
2.4548-2.55290.30251420.26894446X-RAY DIFFRACTION100
2.5529-2.66880.29421420.26674435X-RAY DIFFRACTION100
2.6688-2.80910.30381420.2644423X-RAY DIFFRACTION100
2.8091-2.98460.31171420.26234444X-RAY DIFFRACTION100
2.9846-3.21410.27151440.24354461X-RAY DIFFRACTION100
3.2141-3.53590.27511430.21694462X-RAY DIFFRACTION100
3.5359-4.04380.24431430.19794491X-RAY DIFFRACTION100
4.0438-5.08040.20771470.16074556X-RAY DIFFRACTION100
5.0804-19.8060.23091510.1834717X-RAY DIFFRACTION100

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