[English] 日本語
Yorodumi
- PDB-7asv: Crystal structure of tWHD2 of Rpc5 subunit of human RNA Polymerase III -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7asv
TitleCrystal structure of tWHD2 of Rpc5 subunit of human RNA Polymerase III
ComponentsDNA-directed RNA polymerase III subunit RPC5
KeywordsTRANSCRIPTION / RNA Pol III / RNA Polymerase III / Rpc5
Function / homology
Function and homology information


RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / tRNA transcription by RNA polymerase III / RNA polymerase III complex / defense response to virus ...RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / tRNA transcription by RNA polymerase III / RNA polymerase III complex / defense response to virus / innate immune response / nucleoplasm / cytosol
Similarity search - Function
DNA-directed RNA polymerase III subunit RPC5, C-terminal / DNA-directed RNA polymerase III subunit RPC5 C-terminal / DNA-directed RNA polymerase III subunit Rpc5 / RPC5 protein
Similarity search - Domain/homology
ACETATE ION / DNA-directed RNA polymerase III subunit RPC5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsVannini, A. / Abascal-Palacios, G. / Ramsay, E.P.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Cancer Research UKCR-UK C47547/A21536 United Kingdom
Wellcome Trust200818/Z/16/Z United Kingdom
H2020 Marie Curie Actions of the European Commission655238European Union
CitationJournal: Nat Commun / Year: 2020
Title: Structure of human RNA polymerase III.
Authors: Ewan Phillip Ramsay / Guillermo Abascal-Palacios / Julia L Daiß / Helen King / Jerome Gouge / Michael Pilsl / Fabienne Beuron / Edward Morris / Philip Gunkel / Christoph Engel / Alessandro Vannini /
Abstract: In eukaryotes, RNA Polymerase (Pol) III is specialized for the transcription of tRNAs and other short, untranslated RNAs. Pol III is a determinant of cellular growth and lifespan across eukaryotes. ...In eukaryotes, RNA Polymerase (Pol) III is specialized for the transcription of tRNAs and other short, untranslated RNAs. Pol III is a determinant of cellular growth and lifespan across eukaryotes. Upregulation of Pol III transcription is observed in cancer and causative Pol III mutations have been described in neurodevelopmental disorders and hypersensitivity to viral infection. Here, we report a cryo-EM reconstruction at 4.0 Å of human Pol III, allowing mapping and rationalization of reported genetic mutations. Mutations causing neurodevelopmental defects cluster in hotspots affecting Pol III stability and/or biogenesis, whereas mutations affecting viral sensing are located in proximity to DNA binding regions, suggesting an impairment of Pol III cytosolic viral DNA-sensing. Integrating x-ray crystallography and SAXS, we also describe the structure of the higher eukaryote specific RPC5 C-terminal extension. Surprisingly, experiments in living cells highlight a role for this module in the assembly and stability of human Pol III.
History
DepositionOct 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: DNA-directed RNA polymerase III subunit RPC5
A: DNA-directed RNA polymerase III subunit RPC5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,2684
Polymers162,1502
Non-polymers1182
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-20 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.110, 75.760, 62.400
Angle α, β, γ (deg.)90.000, 103.570, 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 DNA-directed RNA polymerase III subunit RPC5 / RNA polymerase III subunit C5 / DNA-directed RNA polymerase III 80 kDa polypeptide


Mass: 81075.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3E, KIAA1452 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVU0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 3.2-3.8 M Ammonium Acetate and 100 mM Bis-Tris Propane pH 6.5-7

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001Y
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.97942
SYNCHROTRONDiamond I0320.97942, 0.97957, 0.97174
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELMay 15, 2015
DECTRIS PILATUS3 6M2PIXELMay 15, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979571
30.971741
ReflectionResolution: 1.48→30.33 Å / Num. obs: 59533 / % possible obs: 96.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.8
Reflection shellResolution: 1.48→1.52 Å / Rmerge(I) obs: 0.735 / Num. unique obs: 3246
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
PHENIXphenix-1.18.1-3865refinement
xia20.3.8.0data reduction
xia20.3.8.0data scaling
PHENIXphenix-1.18.1-3865phasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→30.33 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.21 --
Rwork0.18 --
obs-59533 96.1 %
Displacement parametersBiso mean: 26.32 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 8 518 2986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01142591
X-RAY DIFFRACTIONf_angle_d1.14653505
X-RAY DIFFRACTIONf_chiral_restr0.0528388
X-RAY DIFFRACTIONf_plane_restr0.0083456
X-RAY DIFFRACTIONf_dihedral_angle_d15.6049987

+
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