[English] 日本語
Yorodumi
- PDB-5uj8: Human Origin Recognition Complex subunits 2 and 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uj8
TitleHuman Origin Recognition Complex subunits 2 and 3
Components
  • Origin recognition complex subunit 2
  • Origin recognition complex subunit 3
KeywordsHYDROLASE / ORC / Replication / ATPase
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / inner kinetochore / nuclear origin of replication recognition complex / nuclear pre-replicative complex / DNA replication preinitiation complex / neural precursor cell proliferation / DNA replication origin binding / regulation of DNA replication ...CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / inner kinetochore / nuclear origin of replication recognition complex / nuclear pre-replicative complex / DNA replication preinitiation complex / neural precursor cell proliferation / DNA replication origin binding / regulation of DNA replication / DNA replication initiation / Activation of the pre-replicative complex / glial cell proliferation / heterochromatin / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / DNA replication / chromosome, telomeric region / nuclear body / centrosome / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus
Similarity search - Function
Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3, N-terminal / Origin recognition complex (ORC) subunit 3 N-terminus / Origin recognition complex subunit 3 insertion domain / Origin recognition complex, subunit 3 / Origin recognition complex subunit 3, winged helix C-terminal / Origin recognition complex winged helix C-terminal / Origin recognition complex subunit 2 / Origin recognition complex, subunit 2
Similarity search - Domain/homology
Origin recognition complex subunit 2 / Origin recognition complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å
AuthorsTocilj, A. / On, K.F. / Elkayam, E. / Joshua-Tor, L.
CitationJournal: Elife / Year: 2017
Title: Structure of the active form of human origin recognition complex and its ATPase motor module.
Authors: Ante Tocilj / Kin Fan On / Zuanning Yuan / Jingchuan Sun / Elad Elkayam / Huilin Li / Bruce Stillman / Leemor Joshua-Tor /
Abstract: Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of ...Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of the active form of human ORC determined by X-ray crystallography and cryo-electron microscopy. The complex is composed of an ORC1/4/5 motor module lobe in an organization reminiscent of the DNA polymerase clamp loader complexes. A second lobe contains the ORC2/3 subunits. The complex is organized as a double-layered shallow corkscrew, with the AAA+ and AAA+-like domains forming one layer, and the winged-helix domains (WHDs) forming a top layer. CDC6 fits easily between ORC1 and ORC2, completing the ring and the DNA-binding channel, forming an additional ATP hydrolysis site. Analysis of the ATPase activity of the complex provides a basis for understanding ORC activity as well as molecular defects observed in Meier-Gorlin Syndrome mutations.
History
DepositionJan 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Origin recognition complex subunit 3
B: Origin recognition complex subunit 3
C: Origin recognition complex subunit 3
D: Origin recognition complex subunit 3
E: Origin recognition complex subunit 2
F: Origin recognition complex subunit 2
G: Origin recognition complex subunit 2
H: Origin recognition complex subunit 2


Theoretical massNumber of molelcules
Total (without water)490,9848
Polymers490,9848
Non-polymers00
Water0
1
A: Origin recognition complex subunit 3
G: Origin recognition complex subunit 2


Theoretical massNumber of molelcules
Total (without water)122,7462
Polymers122,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-20 kcal/mol
Surface area38480 Å2
MethodPISA
2
B: Origin recognition complex subunit 3
E: Origin recognition complex subunit 2


Theoretical massNumber of molelcules
Total (without water)122,7462
Polymers122,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-20 kcal/mol
Surface area38370 Å2
MethodPISA
3
C: Origin recognition complex subunit 3
H: Origin recognition complex subunit 2


Theoretical massNumber of molelcules
Total (without water)122,7462
Polymers122,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-24 kcal/mol
Surface area37780 Å2
MethodPISA
4
D: Origin recognition complex subunit 3
F: Origin recognition complex subunit 2


Theoretical massNumber of molelcules
Total (without water)122,7462
Polymers122,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-21 kcal/mol
Surface area38160 Å2
MethodPISA
5
A: Origin recognition complex subunit 3
G: Origin recognition complex subunit 2

C: Origin recognition complex subunit 3
H: Origin recognition complex subunit 2


Theoretical massNumber of molelcules
Total (without water)245,4924
Polymers245,4924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area8860 Å2
ΔGint-60 kcal/mol
Surface area73370 Å2
MethodPISA
6
B: Origin recognition complex subunit 3
E: Origin recognition complex subunit 2

D: Origin recognition complex subunit 3
F: Origin recognition complex subunit 2


Theoretical massNumber of molelcules
Total (without water)245,4924
Polymers245,4924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area8720 Å2
ΔGint-58 kcal/mol
Surface area73490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.260, 114.961, 316.455
Angle α, β, γ (deg.)90.00, 90.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Origin recognition complex subunit 3 / / Origin recognition complex subunit Latheo


Mass: 82436.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC3, LATHEO, ORC3L
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: Q9UBD5
#2: Protein
Origin recognition complex subunit 2 /


Mass: 40309.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC2, ORC2L
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: Q13416

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 9.5% PEG20000 50mM tri-Sodium-citrate 60mM Citric Acid 10mg/ml HO23 Ratio 1:1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 6→20.07 Å / Num. obs: 15179 / % possible obs: 95 % / Redundancy: 3.4 % / CC1/2: 0.99 / Net I/σ(I): 5.7
Reflection shellResolution: 6→6.21 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1 / CC1/2: 0.422 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XGC - chains B,C

4xgc


Resolution: 6→20.067 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 52.6 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3685 772 5.09 %
Rwork0.318 --
obs0.3205 15179 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6→20.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24148 0 0 0 24148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01324656
X-RAY DIFFRACTIONf_angle_d1.29333360
X-RAY DIFFRACTIONf_dihedral_angle_d11.19314908
X-RAY DIFFRACTIONf_chiral_restr0.0593860
X-RAY DIFFRACTIONf_plane_restr0.0094164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.0012-6.44890.40191580.38042841X-RAY DIFFRACTION93
6.4489-7.06960.38831360.36292887X-RAY DIFFRACTION94
7.0696-8.02920.41791480.36882920X-RAY DIFFRACTION94
8.0292-9.89040.39361600.32322824X-RAY DIFFRACTION91
9.8904-19.47770.32471510.27222903X-RAY DIFFRACTION92

+
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