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- PDB-4dow: Structure of mouse ORC1 BAH domain bound to H4K20me2 -

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Basic information

Entry
Database: PDB / ID: 4dow
TitleStructure of mouse ORC1 BAH domain bound to H4K20me2
Components
  • Histone H4
  • Origin recognition complex subunit 1
KeywordsREPLICATION / DNA replication
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / Assembly of the ORC complex at the origin of replication / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / HDMs demethylate histones ...CDC6 association with the ORC:origin complex / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / Assembly of the ORC complex at the origin of replication / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / Nonhomologous End-Joining (NHEJ) / HDACs deacetylate histones / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / HATs acetylate histones / Orc1 removal from chromatin / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of G0 to G1 transition / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / nuclear origin of replication recognition complex / Estrogen-dependent gene expression / mitotic DNA replication checkpoint signaling / DNA replication initiation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / positive regulation of smooth muscle cell proliferation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / DNA replication / chromosome, telomeric region / protein heterodimerization activity / chromatin binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding
Similarity search - Function
Bromo adjacent homology (BAH) domain / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain ...Bromo adjacent homology (BAH) domain / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / SH3 type barrels. / Histone-fold / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Histone H4 / Origin recognition complex subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSong, J. / Patel, D.J.
CitationJournal: Nature / Year: 2012
Title: The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome.
Authors: Kuo, A.J. / Song, J. / Cheung, P. / Ishibe-Murakami, S. / Yamazoe, S. / Chen, J.K. / Patel, D.J. / Gozani, O.
History
DepositionFeb 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Apr 11, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Origin recognition complex subunit 1
B: Origin recognition complex subunit 1
C: Histone H4
D: Histone H4


Theoretical massNumber of molelcules
Total (without water)40,8574
Polymers40,8574
Non-polymers00
Water3,531196
1
A: Origin recognition complex subunit 1
C: Histone H4


Theoretical massNumber of molelcules
Total (without water)20,4292
Polymers20,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area10040 Å2
MethodPISA
2
B: Origin recognition complex subunit 1
D: Histone H4


Theoretical massNumber of molelcules
Total (without water)20,4292
Polymers20,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-8 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.125, 49.434, 54.376
Angle α, β, γ (deg.)89.93, 102.12, 103.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Origin recognition complex subunit 1 / ORC1


Mass: 18945.902 Da / Num. of mol.: 2 / Fragment: BAH domain (UNP residues 9-170)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Orc1, Orc1l / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9Z1N2
#2: Protein/peptide Histone H4


Mass: 1482.758 Da / Num. of mol.: 2 / Fragment: UNP residues 15-26 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P62806
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2011
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 26059 / Num. obs: 25244 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rsym value: 0.068 / Net I/σ(I): 12.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2482 / Rsym value: 0.253 / % possible all: 95.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→25.864 Å / SU ML: 0.58 / σ(F): 1.97 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 1243 5.06 %
Rwork0.2102 --
obs0.2126 24544 96.9 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.324 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.1768 Å25.6122 Å24.7555 Å2
2---12.284 Å21.5884 Å2
3----3.8928 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 0 196 2876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112753
X-RAY DIFFRACTIONf_angle_d1.4083730
X-RAY DIFFRACTIONf_dihedral_angle_d17.3111042
X-RAY DIFFRACTIONf_chiral_restr0.097399
X-RAY DIFFRACTIONf_plane_restr0.008477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.02810.27941270.23382565X-RAY DIFFRACTION96
2.0281-2.12030.28131260.21962562X-RAY DIFFRACTION96
2.1203-2.2320.24871560.21092590X-RAY DIFFRACTION97
2.232-2.37180.27671380.20872591X-RAY DIFFRACTION97
2.3718-2.55480.29551440.23332576X-RAY DIFFRACTION97
2.5548-2.81160.29221250.23022627X-RAY DIFFRACTION98
2.8116-3.21780.29321380.21682633X-RAY DIFFRACTION98
3.2178-4.05160.22361450.19922608X-RAY DIFFRACTION98
4.0516-25.8660.24031440.19982549X-RAY DIFFRACTION95

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