[English] 日本語
Yorodumi
- PDB-5hog: Crystal structure of the carboxy-terminal domain of yeast Ctf4 bo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hog
TitleCrystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2.
Components
  • DNA polymerase alpha-binding protein
  • Dna2p
KeywordsREPLICATION / DNA replication / adaptor protein / beta-propeller domain
Function / homology
Function and homology information


: / meiotic DNA double-strand break processing / DNA replication, Okazaki fragment processing / establishment of sister chromatid cohesion / Cul8-RING ubiquitin ligase complex / 5'-flap endonuclease activity / DNA double-strand break processing / nuclease activity / single-stranded DNA endodeoxyribonuclease activity / replication fork reversal ...: / meiotic DNA double-strand break processing / DNA replication, Okazaki fragment processing / establishment of sister chromatid cohesion / Cul8-RING ubiquitin ligase complex / 5'-flap endonuclease activity / DNA double-strand break processing / nuclease activity / single-stranded DNA endodeoxyribonuclease activity / replication fork reversal / lagging strand elongation / replication fork protection complex / double-strand break repair via break-induced replication / single-stranded DNA helicase activity / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / DNA helicase activity / telomere maintenance / DNA-templated DNA replication / nucleosome assembly / site of double-strand break / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / DNA helicase / chromosome, telomeric region / Hydrolases; Acting on ester bonds / DNA repair / DNA damage response / chromatin binding / DNA binding / RNA binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / : / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7 helicase-like, C-terminal ...DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / : / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7 helicase-like, C-terminal / AAA domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA replication ATP-dependent helicase/nuclease DNA2 / DNA polymerase alpha-binding protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.092 Å
AuthorsSimon, A.C. / Pellegrini, L.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
Gates Cambridge PhD program United Kingdom
Citation
Journal: Mol.Cell / Year: 2016
Title: Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase.
Authors: Villa, F. / Simon, A.C. / Ortiz Bazan, M.A. / Kilkenny, M.L. / Wirthensohn, D. / Wightman, M. / Matak-Vinkovic, D. / Pellegrini, L. / Labib, K.
#1: Journal: Nature / Year: 2014
Title: A Ctf4 trimer couples the CMG helicase to DNA polymerase alpha in the eukaryotic replisome.
Authors: Simon, A.C. / Zhou, J.C. / Perera, R.L. / van Deursen, F. / Evrin, C. / Ivanova, M.E. / Kilkenny, M.L. / Renault, L. / Kjaer, S. / Matak-Vinkovic, D. / Labib, K. / Costa, A. / Pellegrini, L.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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
D: Dna2p
E: Dna2p


Theoretical massNumber of molelcules
Total (without water)167,1795
Polymers167,1795
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-43 kcal/mol
Surface area50340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.677, 99.551, 218.373
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


Mass: 54447.484 Da / Num. of mol.: 3 / Fragment: UNP residues 450-927
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CTF4, CHL15, POB1, YPR135W, P9659.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01454
#2: Protein/peptide Dna2p


Mass: 1918.045 Da / Num. of mol.: 2 / Fragment: UNP residues 207-223 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to amino acids 207 to 223 of yeast Dna2.
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A0D4IHI3, UniProt: P38859*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.91915 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91915 Å / Relative weight: 1
ReflectionResolution: 3.09→48.98 Å / Num. obs: 36111 / % possible obs: 99.7 % / Redundancy: 6.7 % / Net I/σ(I): 9.8
Reflection shellResolution: 3.09→3.23 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.7 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 3.092→48.98 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3439 5.05 %Random selection
Rwork0.1802 ---
obs0.1826 68099 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.092→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9503 0 0 71 9574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029775
X-RAY DIFFRACTIONf_angle_d0.50513250
X-RAY DIFFRACTIONf_dihedral_angle_d9.4945842
X-RAY DIFFRACTIONf_chiral_restr0.041428
X-RAY DIFFRACTIONf_plane_restr0.0041704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0916-3.1340.36571190.32412413X-RAY DIFFRACTION93
3.134-3.17870.31421360.29942621X-RAY DIFFRACTION100
3.1787-3.22620.27851260.272598X-RAY DIFFRACTION100
3.2262-3.27660.32871300.28962628X-RAY DIFFRACTION100
3.2766-3.33030.36991380.27582546X-RAY DIFFRACTION100
3.3303-3.38770.28591440.24262607X-RAY DIFFRACTION100
3.3877-3.44930.3181310.22732597X-RAY DIFFRACTION100
3.4493-3.51560.26161470.22592630X-RAY DIFFRACTION100
3.5156-3.58730.29031490.21362542X-RAY DIFFRACTION100
3.5873-3.66530.26041340.2152583X-RAY DIFFRACTION100
3.6653-3.75050.25571320.20692608X-RAY DIFFRACTION100
3.7505-3.84430.2121240.19792622X-RAY DIFFRACTION100
3.8443-3.94820.2251280.19592584X-RAY DIFFRACTION100
3.9482-4.06430.31671430.17282611X-RAY DIFFRACTION100
4.0643-4.19540.1935960.15872647X-RAY DIFFRACTION100
4.1954-4.34530.23021540.14622558X-RAY DIFFRACTION100
4.3453-4.51920.19241520.13862581X-RAY DIFFRACTION100
4.5192-4.72470.14641790.132567X-RAY DIFFRACTION100
4.7247-4.97360.17371530.12712593X-RAY DIFFRACTION100
4.9736-5.28480.16051450.13862556X-RAY DIFFRACTION100
5.2848-5.69230.2171390.15162572X-RAY DIFFRACTION100
5.6923-6.26410.19061320.16352631X-RAY DIFFRACTION100
6.2641-7.16810.21081560.17472556X-RAY DIFFRACTION100
7.1681-9.02180.20171190.15072632X-RAY DIFFRACTION100
9.0218-48.98790.21581330.16862577X-RAY DIFFRACTION99

+
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