[English] 日本語
Yorodumi
- PDB-3key: Crystal structure of S. cerevisiae Stn1 C-terminal -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3key
TitleCrystal structure of S. cerevisiae Stn1 C-terminal
ComponentsProtein STN1
KeywordsSTRUCTURAL PROTEIN / butterfly wing-shaped / helix / Chromosomal protein / Phosphoprotein / Telomere
Function / homology
Function and homology information


CST complex / translation elongation factor binding / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / telomere capping / negative regulation of telomere maintenance via telomerase / chromosome, telomeric region
Similarity search - Function
Stn1, N-terminal wHTH domain / Stn1, C-terminal wHTH domain / Stn1, C-terminal, fungi / Stn1, C-terminal domain superfamily / Telomere capping C-terminal wHTH / CST complex subunit Stn1, N-terminal / Telomere regulation protein Stn1 / Ribosomal Protein S8; Chain: A, domain 1 / Arc Repressor Mutant, subunit A / 2-Layer Sandwich ...Stn1, N-terminal wHTH domain / Stn1, C-terminal wHTH domain / Stn1, C-terminal, fungi / Stn1, C-terminal domain superfamily / Telomere capping C-terminal wHTH / CST complex subunit Stn1, N-terminal / Telomere regulation protein Stn1 / Ribosomal Protein S8; Chain: A, domain 1 / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSun, J. / Yu, E.Y. / Yang, Y.T. / Confer, L.A. / Sun, S.H. / Wan, K. / Lue, N.F. / Lei, M.
CitationJournal: Genes Dev. / Year: 2009
Title: Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres.
Authors: Sun, J. / Yu, E.Y. / Yang, Y. / Confer, L.A. / Sun, S.H. / Wan, K. / Lue, N.F. / Lei, M.
History
DepositionOct 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein STN1


Theoretical massNumber of molelcules
Total (without water)21,2371
Polymers21,2371
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.957, 52.957, 186.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Protein STN1


Mass: 21236.600 Da / Num. of mol.: 1 / Fragment: C-terminal fragment: UNP residues 311-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: STN1, YDR082W, D4456, YD8554.15 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P38960
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 6000, 2 M NaCl, 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 16368 / Num. obs: 16057 / % possible obs: 98.8 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 35.3

-
Processing

Software
NameVersionClassification
MAR345CCDdata collection
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å
RfactorNum. reflection
Rfree0.2472 768
Rwork0.2378 -
obs0.2378 15826
all-16057
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 0 73 1487

+
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