[English] 日本語
Yorodumi
- PDB-4c8s: Crystal structure of the C-terminal region of yeast Ctf4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c8s
TitleCrystal structure of the C-terminal region of yeast Ctf4
ComponentsDNA POLYMERASE ALPHA-BINDING PROTEIN
KeywordsDNA REPLICATION / ADAPTOR PROTEIN / BETA PROPELLER DOMAIN
Function / homology
Function and homology information


establishment of sister chromatid cohesion / Cul8-RING ubiquitin ligase complex / replication fork protection complex / double-strand break repair via break-induced replication / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / DNA-templated DNA replication / nucleosome assembly ...establishment of sister chromatid cohesion / Cul8-RING ubiquitin ligase complex / replication fork protection complex / double-strand break repair via break-induced replication / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / DNA-templated DNA replication / nucleosome assembly / mitotic cell cycle / DNA repair / chromatin binding / identical protein binding / nucleus
Similarity search - Function
: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA polymerase alpha-binding protein
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSimon, A.C. / Pellegrini, L.
CitationJournal: Nature / Year: 2014
Title: A Ctf4 Trimer Couples the Cmg Helicase to DNA Polymerase a in the Eukaryotic Replisome
Authors: Simon, A.C. / Zhou, J.C. / Perera, R.L. / Vandeursen, F. / Evrin, C. / Ivanova, M.E. / Kilkenny, M.L. / Renault, L. / Kjaer, S. / Matak-Vinkovic, D. / Labib, K. / Costa, A. / Pellegrini, L.
History
DepositionOct 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA POLYMERASE ALPHA-BINDING PROTEIN
B: DNA POLYMERASE ALPHA-BINDING PROTEIN
C: DNA POLYMERASE ALPHA-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)163,3423
Polymers163,3423
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-28.5 kcal/mol
Surface area50380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.057, 100.251, 219.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein DNA POLYMERASE ALPHA-BINDING PROTEIN / CHROMOSOME REPLICATION PROTEIN CHL15 / CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4 / PROTEIN POB1 / CTF4


Mass: 54447.484 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN, RESIDUES 471-927
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q01454
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.04 Å3/Da / Density % sol: 59.5 % / Description: NONE
Crystal growDetails: 0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 3→49.17 Å / Num. obs: 40196 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 53.98 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 12.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C8H

4c8h


Resolution: 3→48.868 Å / SU ML: 0.32 / σ(F): 1.26 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 3824 5 %
Rwork0.1674 --
obs0.1693 40149 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.6 Å2
Refinement stepCycle: LAST / Resolution: 3→48.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9325 0 0 98 9423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039599
X-RAY DIFFRACTIONf_angle_d0.64913014
X-RAY DIFFRACTIONf_dihedral_angle_d10.2983542
X-RAY DIFFRACTIONf_chiral_restr0.0281399
X-RAY DIFFRACTIONf_plane_restr0.0031671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0380.33741210.28992697X-RAY DIFFRACTION99
3.038-3.0780.28051450.27132647X-RAY DIFFRACTION100
3.078-3.12010.35731190.2592719X-RAY DIFFRACTION100
3.1201-3.16470.30741390.24822643X-RAY DIFFRACTION100
3.1647-3.21190.29751520.2382675X-RAY DIFFRACTION100
3.2119-3.26210.26611420.23862693X-RAY DIFFRACTION100
3.2621-3.31560.30581560.22752620X-RAY DIFFRACTION100
3.3156-3.37270.23741580.21372664X-RAY DIFFRACTION100
3.3727-3.43410.23611400.19592722X-RAY DIFFRACTION100
3.4341-3.50010.24691310.19192637X-RAY DIFFRACTION100
3.5001-3.57150.2341450.18772709X-RAY DIFFRACTION100
3.5715-3.64910.23531200.18072686X-RAY DIFFRACTION100
3.6491-3.7340.21131480.17332658X-RAY DIFFRACTION100
3.734-3.82730.21911500.16092672X-RAY DIFFRACTION100
3.8273-3.93080.20261330.16142657X-RAY DIFFRACTION100
3.9308-4.04640.19611620.15172655X-RAY DIFFRACTION100
4.0464-4.17690.17541420.14182684X-RAY DIFFRACTION100
4.1769-4.32610.15621320.13632664X-RAY DIFFRACTION100
4.3261-4.49920.18671200.13562710X-RAY DIFFRACTION100
4.4992-4.70380.17211580.12322630X-RAY DIFFRACTION100
4.7038-4.95160.13961440.11732705X-RAY DIFFRACTION100
4.9516-5.26150.16781380.12672668X-RAY DIFFRACTION100
5.2615-5.66720.19141270.1352661X-RAY DIFFRACTION100
5.6672-6.23650.16721460.1582675X-RAY DIFFRACTION100
6.2365-7.13650.181470.15752673X-RAY DIFFRACTION100
7.1365-8.98210.17831530.14632650X-RAY DIFFRACTION99
8.9821-48.87420.18451560.16612645X-RAY DIFFRACTION100

+
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://pdbjlvh1.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