[English] 日本語
Yorodumi
- PDB-4dov: Structure of free mouse ORC1 BAH domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dov
TitleStructure of free mouse ORC1 BAH domain
ComponentsOrigin 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 / Orc1 removal from chromatin / positive regulation of G0 to G1 transition / nuclear origin of replication recognition complex / mitotic DNA replication checkpoint signaling / DNA replication initiation / positive regulation of smooth muscle cell proliferation ...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 / Orc1 removal from chromatin / positive regulation of G0 to G1 transition / nuclear origin of replication recognition complex / mitotic DNA replication checkpoint signaling / DNA replication initiation / positive regulation of smooth muscle cell proliferation / DNA replication / chromosome, telomeric region / 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. / 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
Origin recognition complex subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.696 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
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Origin recognition complex subunit 1
C: Origin recognition complex subunit 1


Theoretical massNumber of molelcules
Total (without water)38,0792
Polymers38,0792
Non-polymers00
Water4,324240
1
A: Origin recognition complex subunit 1


Theoretical massNumber of molelcules
Total (without water)19,0401
Polymers19,0401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Origin recognition complex subunit 1


Theoretical massNumber of molelcules
Total (without water)19,0401
Polymers19,0401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.922, 53.916, 71.971
Angle α, β, γ (deg.)90.00, 102.41, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Origin recognition complex subunit 1 / ORC1


Mass: 19039.691 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M 3-(1-pyridino)-1-propane sulfonate, 0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
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: 1.696→30 Å / Num. all: 41317 / Num. obs: 41079 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.064 / Net I/σ(I): 24.3
Reflection shellResolution: 1.696→1.76 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.85 / Num. unique all: 4090 / Rsym value: 0.445 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.696→22.414 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1997 4.87 %RANDOM
Rwork0.2146 ---
obs0.2159 41016 96.9 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.021 Å2 / ksol: 0.412 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.601 Å20 Å20.9148 Å2
2--1.1495 Å20 Å2
3---6.4515 Å2
Refinement stepCycle: LAST / Resolution: 1.696→22.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 0 240 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072538
X-RAY DIFFRACTIONf_angle_d1.123455
X-RAY DIFFRACTIONf_dihedral_angle_d16.956931
X-RAY DIFFRACTIONf_chiral_restr0.085376
X-RAY DIFFRACTIONf_plane_restr0.005444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.696-1.73850.3151280.28642536X-RAY DIFFRACTION90
1.7385-1.78550.31961450.2642803X-RAY DIFFRACTION100
1.7855-1.8380.30191420.25332792X-RAY DIFFRACTION100
1.838-1.89730.25881450.23372795X-RAY DIFFRACTION100
1.8973-1.96510.26181430.22242796X-RAY DIFFRACTION100
1.9651-2.04370.25531450.21662822X-RAY DIFFRACTION100
2.0437-2.13660.25541430.21162801X-RAY DIFFRACTION100
2.1366-2.24920.25831440.21282825X-RAY DIFFRACTION100
2.2492-2.38990.25041440.22162801X-RAY DIFFRACTION100
2.3899-2.57420.30381440.23652831X-RAY DIFFRACTION100
2.5742-2.83280.27931460.23742832X-RAY DIFFRACTION100
2.8328-3.24170.27231440.2212820X-RAY DIFFRACTION100
3.2417-4.08020.21421460.19012858X-RAY DIFFRACTION100
4.0802-22.41560.19151380.20082707X-RAY DIFFRACTION93

+
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