[English] 日本語
Yorodumi
- PDB-7cuj: Crystal structure of fission yeast Ccq1 and Tpz1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cuj
TitleCrystal structure of fission yeast Ccq1 and Tpz1
Components
  • Coiled-coil quantitatively-enriched protein 1
  • Protection of telomeres protein tpz1
KeywordsDNA BINDING PROTEIN / telomere
Function / homology
Function and homology information


telomere-telomerase complex assembly / telomere cap complex / chromosome, telomeric repeat region / meiotic chromosome segregation / meiotic telomere clustering / chromosome, subtelomeric region / mitotic telomere maintenance via semi-conservative replication / shelterin complex / telomere capping / protein localization to chromosome, telomeric region ...telomere-telomerase complex assembly / telomere cap complex / chromosome, telomeric repeat region / meiotic chromosome segregation / meiotic telomere clustering / chromosome, subtelomeric region / mitotic telomere maintenance via semi-conservative replication / shelterin complex / telomere capping / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / telomere maintenance via telomerase / telomere maintenance / molecular adaptor activity / nucleoplasm / nucleus
Similarity search - Function
Adrenocortical dysplasia protein
Similarity search - Domain/homology
Protection of telomeres protein tpz1 / Coiled-coil quantitatively-enriched protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSun, H. / Wu, Z. / Wu, J. / Lei, M.
CitationJournal: Plos Genet. / Year: 2022
Title: Structural insights into Pot1-ssDNA, Pot1-Tpz1 and Tpz1-Ccq1 Interactions within fission yeast shelterin complex.
Authors: Sun, H. / Wu, Z. / Zhou, Y. / Lu, Y. / Lu, H. / Chen, H. / Shi, S. / Zeng, Z. / Wu, J. / Lei, M.
History
DepositionAug 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coiled-coil quantitatively-enriched protein 1
C: Protection of telomeres protein tpz1
B: Coiled-coil quantitatively-enriched protein 1
D: Protection of telomeres protein tpz1


Theoretical massNumber of molelcules
Total (without water)81,6724
Polymers81,6724
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-44 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.300, 71.752, 95.180
Angle α, β, γ (deg.)90.000, 103.890, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Coiled-coil quantitatively-enriched protein 1 / Structural maintenance of chromosomes protein ccq1 / SMC protein ccq1


Mass: 35256.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: ccq1, SPCC188.07 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q10432
#2: Protein/peptide Protection of telomeres protein tpz1 / Meiotically up-regulated gene 169 protein


Mass: 5579.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tpz1, mug169, SPAC6F6.16c, SPAC6F6.18c / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14246
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.37 Å3/Da / Density % sol: 48.02 % / Mosaicity: 0.41 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.8
Details: 15% PEG4000, 200mM potassium chloride, 50mM magnesium chloride and 50mM Tris-HCl

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL18U110.97853
SYNCHROTRONSSRF BL19U120.97853
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELMay 15, 2015
DECTRIS PILATUS 6M2PIXELMay 15, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978531
21
ReflectionResolution: 2.4→50 Å / Num. obs: 29579 / % possible obs: 98.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.03 / Rrim(I) all: 0.066 / Χ2: 0.913 / Net I/σ(I): 8.1 / Num. measured all: 131622
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4940.59327460.860.3180.6760.94692
2.49-2.594.30.49228860.9240.2550.5570.89998.2
2.59-2.74.60.36829730.9650.1850.4130.95599.7
2.7-2.854.60.2629500.9760.1320.2930.95499.7
2.85-3.024.60.16629610.9890.0840.1870.976100
3.02-3.264.30.10930160.9920.0570.1230.998100
3.26-3.584.60.07229810.9950.0360.0811.022100
3.58-4.14.70.0529830.9970.0250.0560.964100
4.1-5.174.30.03930060.9970.020.0440.8299.9
5.17-504.50.03230770.9980.0160.0360.60499.8

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→38.87 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 19.516 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 1240 4.9 %RANDOM
Rwork0.1967 ---
obs0.1995 23849 83.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.5 Å2 / Biso mean: 54.986 Å2 / Biso min: 12.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å21.85 Å2
2---0.4 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 2.4→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 0 80 4806
Biso mean---40.22 -
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124839
X-RAY DIFFRACTIONr_angle_refined_deg0.8311.6216545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9465578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22922.802232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50815850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5591520
X-RAY DIFFRACTIONr_chiral_restr0.0730.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023595
X-RAY DIFFRACTIONr_rigid_bond_restr0.55434839
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 56 -
Rwork0.199 958 -
all-1014 -
obs--46.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5026-0.76943.112.3094-1.05853.28840.01060.16480.1079-0.4479-0.04250.420.12270.01690.03190.1001-0.0091-0.09820.08240.01140.1097-25.800542.30992.8889
27.9572-2.11560.17521.0884-0.16022.27990.26990.1381-0.37310.0546-0.00550.27370.3371-0.4218-0.26440.1005-0.0556-0.020.08460.04210.1621-18.909428.911822.4882
32.9737-1.30292.7272.7208-1.03473.6521-0.03840.11760.18960.6463-0.0688-0.4583-0.01980.15590.10720.1882-0.0083-0.11550.00730.00810.089414.817729.69643.213
41.5366-0.86032.47533.0601-3.76289.3832-0.3474-0.21330.48440.57650.13590.1436-0.6119-0.19780.21150.16510.0626-0.06540.0429-0.0740.2303-4.536643.787132.6234
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A132 - 439
2X-RAY DIFFRACTION2C429 - 466
3X-RAY DIFFRACTION3B132 - 439
4X-RAY DIFFRACTION4D427 - 462

+
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