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- PDB-3g65: Crystal Structure of the Human Rad9-Rad1-Hus1 DNA Damage Checkpoi... -

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Basic information

Entry
Database: PDB / ID: 3g65
TitleCrystal Structure of the Human Rad9-Rad1-Hus1 DNA Damage Checkpoint Complex
Components
  • Cell cycle checkpoint control protein RAD9A
  • Cell cycle checkpoint protein RAD1
  • Checkpoint protein HUS1
KeywordsCELL CYCLE / PCNA / DNA BINDING CLAMP / DNA damage / DNA repair / Exonuclease / Hydrolase / Nuclease / Nucleus / Phosphoprotein
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
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDore, A.S. / Kilkenny, M.L. / Rzechorzek, N.J. / Pearl, L.H.
CitationJournal: Mol.Cell / Year: 2009
Title: Crystal structure of the rad9-rad1-hus1 DNA damage checkpoint complex--implications for clamp loading and regulation.
Authors: Dore, A.S. / Kilkenny, M.L. / Rzechorzek, N.J. / Pearl, L.H.
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Cell cycle checkpoint protein RAD1
C: Checkpoint protein HUS1


Theoretical massNumber of molelcules
Total (without water)96,0383
Polymers96,0383
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-23 kcal/mol
Surface area35850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.246, 70.673, 83.151
Angle α, β, γ (deg.)90.00, 99.51, 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: 32452.266 Da / Num. of mol.: 1 / Fragment: UNP residues 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD9, RAD9A / Plasmid: pFBDM / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q99638, exodeoxyribonuclease III
#2: 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 / Plasmid: pFBDM / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60671, exodeoxyribonuclease III
#3: Protein Checkpoint protein HUS1 / hHUS1


Mass: 31731.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUS1 / Plasmid: pFBDM / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60921
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 17% PEG 2000-Mme, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF ID2921.0716
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 7, 2007
ADSC QUANTUM 315r2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
21.07161
ReflectionResolution: 2.9→82 Å / Num. all: 19109 / Num. obs: 18454 / % possible obs: 97.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.115 / Net I/σ(I): 3.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2593 / Rsym value: 0.326 / % possible all: 94

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AXC

1axc


Resolution: 2.9→82 Å / SU ML: 0.4 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 942 5.11 %RANDOM
Rwork0.2208 ---
obs0.2236 18445 96.52 %-
all-19109 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.893 Å2 / ksol: 0.3 e/Å3
Refinement stepCycle: LAST / Resolution: 2.9→82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6068 0 0 82 6150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.03590.35671160.30482232X-RAY DIFFRACTION87
3.0359-3.22610.33411440.28052533X-RAY DIFFRACTION98
3.2261-3.47520.33651380.23862515X-RAY DIFFRACTION98
3.4752-3.8250.30111130.21382517X-RAY DIFFRACTION98
3.825-4.37840.2331360.19672534X-RAY DIFFRACTION97
4.3784-5.51620.22461460.16622525X-RAY DIFFRACTION98
5.5162-82.04250.24791490.23062647X-RAY DIFFRACTION100
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)
10.0674-0.004-0.01540.0331-0.0470.099-0.04210.26060.18920.91010.2722-0.5650.7344-0.4210-0.3819-0.92770.2331-0.36090.07060.01821.4351-17.69381.9714
2-0.04470.0376-0.0517-0.0480.0245-0.0117-0.001-0.1444-0.0977-0.02690.15330.14120.0006-0.21210-0.1574-0.59190.15860.5677-0.4543-0.0503-7.158-16.3134-16.4435
3-0.0140.1921-0.04490.12050.15360.0795-0.24540.30250.3743-0.1401-0.0105-0.07530.6754-0.4038-00.0979-0.14840.03650.2748-0.09040.2049.0978-8.4569-22.8015
40.08140.07760.00830.0921-0.07890.1356-0.3294-0.1862-0.02260.26610.22050.0363-0.26870.0041-00.2345-0.004-0.10040.1355-0.00570.149929.219215.242326.6113
5-0.04220.0208-0.0251-0.0134-0.0168-0.0067-0.1015-0.05530.06270.1559-0.2133-0.04060.3207-0.3077-00.76050.14310.17580.07790.3123-0.564913.06919.161937.5249
60.05810.0402-0.09520.13070.1093-0.0569-0.11740.4414-0.08640.0806-0.045-0.07270.1467-0.22700.1978-0.06190.03760.29020.03910.155312.1975-6.795426.3727
70.18710.10550.03220.0492-0.03430.1576-0.04170.005-0.4636-0.23050.0849-0.1206-0.30980.131700.2001-0.09570.05830.1681-0.02710.258729.351311.7624-24.1868
80.01660.0394-0.0113-0.0241-0.06940.0070.11430.263-0.4203-0.8606-0.62070.2772-0.0006-0.090900.348-0.45440.0597-0.44770.3352-0.060131.956831.332-19.5237
90.0744-0.08860.10120.1921-0.16550.18370.1602-0.06810.0530.0415-0.097-0.2808-0.51580.3352-00.2328-0.129-0.02910.19540.06030.209635.785625.3671.6778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:126A1 - 126
2X-RAY DIFFRACTION2chain A and resid 127:143A127 - 143
3X-RAY DIFFRACTION3chain A and resid 144:276A144 - 27
4X-RAY DIFFRACTION4chain B and resid 15:135B - A15 - 135
5X-RAY DIFFRACTION5chain B and resid 136:153B136 - 153
6X-RAY DIFFRACTION6chain B and resid 154:280B154 - 280
7X-RAY DIFFRACTION7chain C and resid 1:134C1 - 134
8X-RAY DIFFRACTION8chain C and resid 135:158C135 - 158
9X-RAY DIFFRACTION9chain C and resid 159:280C159 - 280

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