[English] 日本語
Yorodumi
- PDB-8j8p: Structure of the four-component Paf1 complex from Saccharomyces e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8j8p
TitleStructure of the four-component Paf1 complex from Saccharomyces eubayanus
Components
  • CDC73-like protein
  • CTR9-like protein
  • PAF1-like protein
  • RTF1-like protein
KeywordsTRANSCRIPTION / transcription elongation factor / the polymerase associated factor 1 (Paf1) complex
Function / homology
Function and homology information


Cdc73/Paf1 complex / transcription elongation by RNA polymerase II / regulation of DNA-templated transcription / protein-containing complex / DNA binding / nucleus
Similarity search - Function
Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / RNA polymerase II associated factor Paf1 / Paf1 / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal ...Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / RNA polymerase II associated factor Paf1 / Paf1 / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal / Tetratricopeptide repeat / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
CDC73-like protein / CTR9-like protein / RTF1-like protein / PAF1-like protein
Similarity search - Component
Biological speciesSaccharomyces eubayanus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsWang, Z. / Qin, Y. / Zhou, Y. / Cao, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870725 China
National Natural Science Foundation of China (NSFC)32125008 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Basis of the Transcriptional Elongation Factor Paf1 Core Complex from Saccharomyces eubayanus .
Authors: Qin, Y. / Zhou, Y. / Cao, Y. / Ren, Y. / Deng, P. / Jiang, J. / Wang, Z.
History
DepositionMay 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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
C: CTR9-like protein
A: CDC73-like protein
P: PAF1-like protein
R: RTF1-like protein


Theoretical massNumber of molelcules
Total (without water)135,3794
Polymers135,3794
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19780 Å2
ΔGint-130 kcal/mol
Surface area56290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.775, 88.480, 127.775
Angle α, β, γ (deg.)90.000, 97.272, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein CTR9-like protein


Mass: 104814.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_2263 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RHL9
#2: Protein CDC73-like protein


Mass: 8488.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_3914 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RF82
#3: Protein PAF1-like protein


Mass: 12700.642 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_1302 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RM45
#4: Protein RTF1-like protein


Mass: 9374.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_1738 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RIY1
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium citrate tribasic pH 7.0; 25% w/v Polyethylene glyco 3,350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 43763 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 64.74 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.1
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 2197 / CC1/2: 0.706

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→34.47 Å / SU ML: 0.3742 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.1952 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2625 2125 4.87 %
Rwork0.2251 41549 -
obs0.227 43674 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9049 0 0 79 9128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00779208
X-RAY DIFFRACTIONf_angle_d1.028412405
X-RAY DIFFRACTIONf_chiral_restr0.0661387
X-RAY DIFFRACTIONf_plane_restr0.00471591
X-RAY DIFFRACTIONf_dihedral_angle_d27.66523543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.36321400.31562681X-RAY DIFFRACTION96.05
2.76-2.830.32091480.29282699X-RAY DIFFRACTION99.68
2.83-2.910.30241220.27842787X-RAY DIFFRACTION99.79
2.91-2.990.29851560.27392786X-RAY DIFFRACTION99.83
2.99-3.090.30481480.27062742X-RAY DIFFRACTION99.93
3.09-3.20.29971220.26912768X-RAY DIFFRACTION99.9
3.2-3.330.30421510.25152755X-RAY DIFFRACTION99.9
3.33-3.480.32541460.24552780X-RAY DIFFRACTION99.9
3.48-3.660.27131510.21342788X-RAY DIFFRACTION99.9
3.66-3.890.25621310.20842757X-RAY DIFFRACTION99.83
3.89-4.190.23381370.19722796X-RAY DIFFRACTION99.69
4.19-4.610.23411440.19162780X-RAY DIFFRACTION99.9
4.61-5.270.24811580.20822779X-RAY DIFFRACTION99.8
5.27-6.640.3051340.25862822X-RAY DIFFRACTION99.93
6.64-34.470.21351370.2022829X-RAY DIFFRACTION98.24

+
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