[English] 日本語
Yorodumi
- PDB-1zhi: Complex of the S. cerevisiae Orc1 and Sir1 interacting domains -

+
Open data


ID or keywords:

Loading...

-
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 / maintenance of rDNA / Assembly of the ORC complex at the origin of replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / nucleosome organization / nuclear pre-replicative complex / chromatin silencing complex / Activation of ATR in response to replication stress ...CDC6 association with the ORC:origin complex / maintenance of rDNA / Assembly of the ORC complex at the origin of replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / nucleosome organization / nuclear pre-replicative complex / chromatin silencing complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / Orc1 removal from chromatin / DNA replication origin binding / nucleosome binding / chromosome, centromeric region / DNA replication initiation / heterochromatin formation / chromatin binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / metal ion binding
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 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 domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more