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- PDB-1zhi: Complex of the S. cerevisiae Orc1 and Sir1 interacting domains -

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Basic information

Entry
Database: PDB / ID: 1zhi
TitleComplex of the S. cerevisiae Orc1 and Sir1 interacting domains
Components
  • Origin recognition complex subunit 1
  • Regulatory protein SIR1
KeywordsTranscription/Replication / protein complex / BAH domain / OIR domain / Transcription-Replication COMPLEX
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / maintenance of rDNA / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nuclear pre-replicative complex / Activation of ATR in response to replication stress / chromatin silencing complex ...CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / maintenance of rDNA / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nuclear pre-replicative complex / Activation of ATR in response to replication stress / chromatin silencing complex / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / DNA replication origin binding / chromosome, centromeric region / DNA replication initiation / nucleosome binding / heterochromatin formation / chromatin binding / ATP hydrolysis activity / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
Sir1, ORC-binding domain / ORC1-binding domain / Sir1, ORC-binding domain / Bromo adjacent homology (BAH) domain / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain ...Sir1, ORC-binding domain / ORC1-binding domain / Sir1, ORC-binding domain / Bromo adjacent homology (BAH) domain / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / SH3 type barrels. / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Regulatory protein SIR1 / Origin recognition complex subunit 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHou, Z. / Bernstein, D.A. / Fox, C.A. / Keck, J.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing.
Authors: Hou, Z. / Bernstein, D.A. / Fox, C.A. / Keck, J.L.
History
DepositionApr 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Origin recognition complex subunit 1
B: Regulatory protein SIR1


Theoretical massNumber of molelcules
Total (without water)42,2612
Polymers42,2612
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.151, 72.151, 310.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Origin recognition complex subunit 1 / / Origin recognition complex protein 120 kDa subunit


Mass: 26100.674 Da / Num. of mol.: 1 / Fragment: BAH domain of Orc1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ORC1 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P54784
#2: Protein Regulatory protein SIR1 / Silent information regulator 1


Mass: 16160.791 Da / Num. of mol.: 1 / Fragment: OIR* domain of Sir1 / Mutation: Cys593Ala
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR1 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P21691
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.86 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris, NaCl, Ammonium Sulfate, pH 7.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2004
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→62 Å / Num. all: 14005 / Num. obs: 14005 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.85 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→18 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.867 / SU B: 12.766 / SU ML: 0.266 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.683 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29323 696 5 %RANDOM
Rwork0.23082 ---
all0.2338 13146 --
obs0.2338 13146 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.218 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.7→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 0 66 2699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222691
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9643645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.475317
X-RAY DIFFRACTIONr_chiral_restr0.0770.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022037
X-RAY DIFFRACTIONr_nbd_refined0.220.21083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.24
X-RAY DIFFRACTIONr_mcbond_it0.5831.51600
X-RAY DIFFRACTIONr_mcangle_it1.09722597
X-RAY DIFFRACTIONr_scbond_it1.3631091
X-RAY DIFFRACTIONr_scangle_it2.3084.51048
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.372 48
Rwork0.295 913
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)
14.55270.5728-2.08934.6589-0.50413.21560.2629-0.25680.6490.7224-0.20070.2612-0.54680.0655-0.06220.2959-0.0776-0.02220.0953-0.08040.1008-16.693845.409115.2004
26.4652-4.82624.07735.0823-3.5364.13040.35990.1683-0.2149-0.0971-0.3144-0.22130.22120.19-0.04550.1535-0.0761-0.0950.2510.10610.26565.490922.8791105.2115
32.00930.38870.49220.8753-0.42520.88540.09880.02280.19660.2329-0.0906-0.1859-0.04210.1015-0.00820.1423-0.0931-0.03190.12420.05380.0485-7.548235.5423107.1004
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 21416 - 220
2X-RAY DIFFRACTION2BB487 - 61114 - 138
3X-RAY DIFFRACTION3BD1 - 66

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