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- PDB-3a1j: Crystal structure of the human Rad9-Hus1-Rad1 complex -

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Basic information

Entry
Database: PDB / ID: 3a1j
TitleCrystal structure of the human Rad9-Hus1-Rad1 complex
Components
  • Cell cycle checkpoint control protein RAD9A
  • Cell cycle checkpoint protein RAD1
  • Checkpoint protein HUS1
KeywordsHYDROLASE/CELL CYCLE / DNA damage / checkpoint / DNA repair / Exonuclease / Hydrolase / Nuclease / Nucleus / Phosphoprotein / Polymorphism / Cytoplasm / Alternative splicing / HYDROLASE-CELL CYCLE COMPLEX
Function / homology
Function and homology information


meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / 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 / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / 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 / 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 / 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 / nucleolus / protein kinase binding / enzyme binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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
sucrose / Cell cycle checkpoint protein RAD1 / Checkpoint protein HUS1 / Cell cycle checkpoint control protein RAD9A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSohn, S.Y. / Cho, Y.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of the Human Rad9-Hus1-Rad1 Clamp
Authors: Sohn, S.Y. / Cho, Y.
History
DepositionApr 8, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2564
Polymers91,9143
Non-polymers3421
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-14 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.154, 70.776, 86.661
Angle α, β, γ (deg.)90.00, 99.20, 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: 29609.406 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Gene: Rad9(1-272) / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q99638, exodeoxyribonuclease III
#2: Protein Checkpoint protein HUS1 / hHUS1


Mass: 32292.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Gene: HUS1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O60921
#3: Protein Cell cycle checkpoint protein RAD1 / hRAD1 / DNA repair exonuclease rad1 homolog / Rad1-like DNA damage checkpoint protein


Mass: 30012.166 Da / Num. of mol.: 1 / Fragment: residues 13-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Gene: RAD1 / Plasmid: pCOLA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O60671, exodeoxyribonuclease III
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 15% PEG 3350, 0.18M KCl, 0.16M guanidine hydrochloride, 0.33M ZWITTERGENT 3-08, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 32031 / Num. obs: 31999 / % possible obs: 99.9 % / Biso Wilson estimate: 38.7 Å2 / Rsym value: 0.09 / Net I/σ(I): 5.8
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.278 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 116907 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1537 5 %RANDOM
Rwork0.209 ---
obs0.209 30943 96.2 %-
all-32031 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.3871 Å2 / ksol: 0.33839 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å2-1.54 Å2
2--2.38 Å20 Å2
3----0.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6258 0 23 186 6467
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.842
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 251 5.3 %
Rwork0.275 4526 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3suc_paramsuc_top

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