[English] 日本語
Yorodumi
- PDB-3c0t: Structure of the Schizosaccharomyces pombe Mediator subcomplex Me... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c0t
TitleStructure of the Schizosaccharomyces pombe Mediator subcomplex Med8C/18
Components
  • Mediator of RNA polymerase II transcription subunit 18
  • Mediator of RNA polymerase II transcription subunit 8
KeywordsTRANSCRIPTION / BETA BARREL / CHANNEL / PROTEIN-PROTEIN COMPLEX / Activator / Nucleus / Transcription regulation
Function / homology
Function and homology information


core mediator complex / mediator complex / termination of RNA polymerase II transcription / positive regulation of transcription initiation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / Mediator complex, subunit Med8, fungi/metazoa / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex, subunit Med18 / Med18 protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 8
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLariviere, L. / Seizl, M. / van Wageningen, S. / Roether, S. / van de Pasch, L. / Feldmann, H. / Straesser, K. / Hahn, S. / Holstege, C.P. / Cramer, P.
CitationJournal: Genes Dev. / Year: 2008
Title: Structure-system correlation identifies a gene regulatory Mediator submodule
Authors: Lariviere, L. / Seizl, M. / van Wageningen, S. / Rother, S. / van de Pasch, L. / Feldmann, H. / Strasser, K. / Hahn, S. / Holstege, F.C.P. / Cramer, P.
History
DepositionJan 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 18
B: Mediator of RNA polymerase II transcription subunit 8


Theoretical massNumber of molelcules
Total (without water)27,9162
Polymers27,9162
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-12.8 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.016, 111.016, 68.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18 / Cell separation protein sep11 / RNA polymerase II mediator complex protein pmc6


Mass: 24056.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O14198
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 8 / Mediator complex subunit 8 / Cell separation protein sep15


Mass: 3859.357 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP Residues 180-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O94646
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.37 Å3/Da / Density % sol: 71.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris pH 8.5, 2M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2006
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 19282 / Num. obs: 19282 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Rsym value: 0.084 / Net I/σ(I): 21.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 2806 / Rsym value: 0.379 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHASERphasing
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model is the structure of Med18 alone, which has not been deposited.

Resolution: 2.4→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2314 937 RANDOM
Rwork0.211 --
all-19282 -
obs-19282 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 0 62 1884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.293
X-RAY DIFFRACTIONc_bond_d0.006

+
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