[English] 日本語
Yorodumi
- PDB-6s1c: P3221 crystal form of the Ctf18-1-8/Pol2(1-528) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s1c
TitleP3221 crystal form of the Ctf18-1-8/Pol2(1-528) complex
Components
  • Chromosome transmission fidelity protein 18
  • Chromosome transmission fidelity protein 8
  • DNA polymerase epsilon catalytic subunit A
  • Sister chromatid cohesion protein DCC1
KeywordsREPLICATION / DNA polymerase / PCNA loader / protein complex
Function / homology
Function and homology information


maintenance of mitotic sister chromatid cohesion / gene conversion / DNA replication initiation / epsilon DNA polymerase complex / Ctf18 RFC-like complex / telomere tethering at nuclear periphery / maintenance of DNA trinucleotide repeats / SUMO binding / nucleotide-excision repair, DNA gap filling / Activation of the pre-replicative complex ...maintenance of mitotic sister chromatid cohesion / gene conversion / DNA replication initiation / epsilon DNA polymerase complex / Ctf18 RFC-like complex / telomere tethering at nuclear periphery / maintenance of DNA trinucleotide repeats / SUMO binding / nucleotide-excision repair, DNA gap filling / Activation of the pre-replicative complex / DNA replication proofreading / Termination of translesion DNA synthesis / single-stranded DNA 3'-5' DNA exonuclease activity / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / mitotic sister chromatid cohesion / leading strand elongation / nuclear replication fork / Dual incision in TC-NER / chromosome, centromeric region / DNA replication initiation / error-prone translesion synthesis / base-excision repair, gap-filling / replication fork / double-strand break repair via homologous recombination / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / double-strand break repair / mitotic cell cycle / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / mRNA binding / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / ATP binding / nucleus
Similarity search - Function
Chromosome transmission fidelity protein 8 / Ctf8 / Sister chromatid cohesion protein Dcc1 / Sister chromatid cohesion protein Dcc1 / : / : / DNA polymerase epsilon catalytic subunit A, thumb domain / Zinc finger domain of DNA polymerase-epsilon / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit ...Chromosome transmission fidelity protein 8 / Ctf8 / Sister chromatid cohesion protein Dcc1 / Sister chromatid cohesion protein Dcc1 / : / : / DNA polymerase epsilon catalytic subunit A, thumb domain / Zinc finger domain of DNA polymerase-epsilon / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / : / DNA polymerase family B, thumb domain / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribonuclease H superfamily / Ribonuclease H-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA polymerase epsilon catalytic subunit A / Sister chromatid cohesion protein DCC1 / Chromosome transmission fidelity protein 8 / Chromosome transmission fidelity protein 18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.1 Å
AuthorsGrabarczyk, D.B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGR 5152/3-1 Germany
CitationJournal: Nucleic Acids Res / Year: 2020
Title: Ctf18-RFC and DNA Pol ϵ form a stable leading strand polymerase/clamp loader complex required for normal and perturbed DNA replication.
Authors: Katy Stokes / Alicja Winczura / Boyuan Song / Giacomo De Piccoli / Daniel B Grabarczyk /
Abstract: The eukaryotic replisome must faithfully replicate DNA and cope with replication fork blocks and stalling, while simultaneously promoting sister chromatid cohesion. Ctf18-RFC is an alternative PCNA ...The eukaryotic replisome must faithfully replicate DNA and cope with replication fork blocks and stalling, while simultaneously promoting sister chromatid cohesion. Ctf18-RFC is an alternative PCNA loader that links all these processes together by an unknown mechanism. Here, we use integrative structural biology combined with yeast genetics and biochemistry to highlight the specific functions that Ctf18-RFC plays within the leading strand machinery via an interaction with the catalytic domain of DNA Pol ϵ. We show that a large and unusually flexible interface enables this interaction to occur constitutively throughout the cell cycle and regardless of whether forks are replicating or stalled. We reveal that, by being anchored to the leading strand polymerase, Ctf18-RFC can rapidly signal fork stalling to activate the S phase checkpoint. Moreover, we demonstrate that, independently of checkpoint signaling or chromosome cohesion, Ctf18-RFC functions in parallel to Chl1 and Mrc1 to protect replication forks and cell viability.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase epsilon catalytic subunit A
E: DNA polymerase epsilon catalytic subunit A
B: Sister chromatid cohesion protein DCC1
C: Chromosome transmission fidelity protein 8
D: Chromosome transmission fidelity protein 18
F: Sister chromatid cohesion protein DCC1
G: Chromosome transmission fidelity protein 8
H: Chromosome transmission fidelity protein 18


Theoretical massNumber of molelcules
Total (without water)251,3988
Polymers251,3988
Non-polymers00
Water00
1
A: DNA polymerase epsilon catalytic subunit A
B: Sister chromatid cohesion protein DCC1
C: Chromosome transmission fidelity protein 8
D: Chromosome transmission fidelity protein 18


Theoretical massNumber of molelcules
Total (without water)125,6994
Polymers125,6994
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA polymerase epsilon catalytic subunit A
F: Sister chromatid cohesion protein DCC1
G: Chromosome transmission fidelity protein 8
H: Chromosome transmission fidelity protein 18


Theoretical massNumber of molelcules
Total (without water)125,6994
Polymers125,6994
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.334, 126.334, 378.427
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNGLNGLN(chain 'A' and (resid 29 through 90 or resid 113...AA29 - 5954 - 84
121GLYGLYGLUGLU(chain 'A' and (resid 29 through 90 or resid 113...AA77 - 90102 - 115
131GLYGLYTYRTYR(chain 'A' and (resid 29 through 90 or resid 113...AA113 - 138138 - 163
141VALVALSERSER(chain 'A' and (resid 29 through 90 or resid 113...AA149 - 166174 - 191
151SERSERLEULEU(chain 'A' and (resid 29 through 90 or resid 113...AA192 - 205217 - 230
161TYRTYRGLNGLN(chain 'A' and (resid 29 through 90 or resid 113...AA245 - 523270 - 548
271ASNASNGLNGLN(chain 'E' and (resid 29 through 59 or resid 77 through 524))EB29 - 5954 - 84
281GLYGLYGLUGLU(chain 'E' and (resid 29 through 59 or resid 77 through 524))EB77 - 90102 - 115
291GLYGLYTYRTYR(chain 'E' and (resid 29 through 59 or resid 77 through 524))EB113 - 138138 - 163
2101VALVALSERSER(chain 'E' and (resid 29 through 59 or resid 77 through 524))EB149 - 166174 - 191
2111SERSERLEULEU(chain 'E' and (resid 29 through 59 or resid 77 through 524))EB192 - 205217 - 230
2121TYRTYRGLNGLN(chain 'E' and (resid 29 through 59 or resid 77 through 524))EB245 - 523270 - 548
1132SERSERASNASN(chain 'B' and (resid 2 through 201 or resid 252 through 380))BC2 - 1202 - 120
1142VALVALSERSER(chain 'B' and (resid 2 through 201 or resid 252 through 380))BC143 - 171143 - 171
1152CYSCYSLEULEU(chain 'B' and (resid 2 through 201 or resid 252 through 380))BC178 - 201178 - 201
1162LEULEULYSLYS(chain 'B' and (resid 2 through 201 or resid 252 through 380))BC252 - 307252 - 307
1172LYSLYSARGARG(chain 'B' and (resid 2 through 201 or resid 252 through 380))BC311 - 380311 - 380
2182SERSERASNASNchain 'F'FF2 - 1202 - 120
2192VALVALSERSERchain 'F'FF143 - 171143 - 171
2202CYSCYSLEULEUchain 'F'FF178 - 201178 - 201
2212LEULEULYSLYSchain 'F'FF252 - 307252 - 307
2222LYSLYSARGARGchain 'F'FF311 - 380311 - 380
1233PROPROILEILEchain 'C'CD2 - 1322 - 132
2243PROPROILEILEchain 'G'GG2 - 1322 - 132
1254ILEILEGLUGLUchain 'D'DE718 - 74110 - 33
2264ILEILEGLUGLUchain 'H'HH718 - 74110 - 33

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein DNA polymerase epsilon catalytic subunit A / DNA polymerase II subunit A


Mass: 62516.250 Da / Num. of mol.: 2 / Mutation: D290A, E292A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: POL2, DUN2, YNL262W, N0825 / Production host: Escherichia coli (E. coli) / References: UniProt: P21951, DNA-directed DNA polymerase
#2: Protein Sister chromatid cohesion protein DCC1 / Defective in sister chromatid cohesion protein 1


Mass: 44133.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: DCC1, YCL016C, YCL16C / Production host: Escherichia coli (E. coli) / References: UniProt: P25559
#3: Protein Chromosome transmission fidelity protein 8


Mass: 15189.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CTF8, YHR191C / Production host: Escherichia coli (E. coli) / References: UniProt: P38877
#4: Protein/peptide Chromosome transmission fidelity protein 18


Mass: 3859.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CTF18, CHL12, YMR078C, YM9582.03C / Production host: Escherichia coli (E. coli) / References: UniProt: P49956
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 14% PEG 20000, 0.1 M HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 6.1→19.97 Å / Num. obs: 8632 / % possible obs: 97.2 % / Redundancy: 9.5 % / Biso Wilson estimate: 453.45 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.2
Reflection shellResolution: 6.1→6.82 Å / Redundancy: 10 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2471 / CC1/2: 0.362 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M8O, 5OKC and 5OKI

4m8o

5okc

5oki


Resolution: 6.1→19.97 Å / SU ML: 1.4327 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.5751
RfactorNum. reflection% reflectionSelection details
Rfree0.3326 840 9.78 %Random selection
Rwork0.2746 ---
obs0.28 8593 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 511.41 Å2
Refinement stepCycle: LAST / Resolution: 6.1→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14378 0 0 0 14378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003214713
X-RAY DIFFRACTIONf_angle_d0.738619892
X-RAY DIFFRACTIONf_chiral_restr0.04822184
X-RAY DIFFRACTIONf_plane_restr0.00562540
X-RAY DIFFRACTIONf_dihedral_angle_d13.53618864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.1-6.470.43251430.39471247X-RAY DIFFRACTION99.78
6.47-6.950.41531460.37771261X-RAY DIFFRACTION100
6.95-7.610.46161340.34221278X-RAY DIFFRACTION100
7.61-8.640.35131330.29651292X-RAY DIFFRACTION100
8.64-10.60.30911530.25281302X-RAY DIFFRACTION100
10.6-19.970.29421310.24521373X-RAY DIFFRACTION99.6

+
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