[English] 日本語
Yorodumi
- PDB-6f4a: Yeast mitochondrial RNA degradosome complex mtEXO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f4a
TitleYeast mitochondrial RNA degradosome complex mtEXO
Components
  • Exoribonuclease II, mitochondrial
  • RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')
  • Suv3 helicase
KeywordsHYDROLASE / RNA degradation / mitochondria / nuclease / helicase / protein complex
Function / homology
Function and homology information


mitochondrial chromosome / mitochondrial degradosome / mitochondrial RNA catabolic process / exoribonuclease II activity / mitochondrial DNA replication / Group I intron splicing / RNA nuclease activity / RNA helicase activity / RNA helicase / mitochondrion ...mitochondrial chromosome / mitochondrial degradosome / mitochondrial RNA catabolic process / exoribonuclease II activity / mitochondrial DNA replication / Group I intron splicing / RNA nuclease activity / RNA helicase activity / RNA helicase / mitochondrion / RNA binding / ATP binding
Similarity search - Function
Mitochondrial degradasome RNA helicase subunit, C-terminal domain / Mitochondrial degradasome RNA helicase subunit C terminal / Ribonuclease II/R / RNB domain / RNB / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily ...Mitochondrial degradasome RNA helicase subunit, C-terminal domain / Mitochondrial degradasome RNA helicase subunit C terminal / Ribonuclease II/R / RNB domain / RNB / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / Exoribonuclease II, mitochondrial / RNB domain-containing protein / RNA helicase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsRazew, M. / Nowak, E. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre Poland00463 Poland
CitationJournal: Nat Commun / Year: 2018
Title: Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components.
Authors: Razew, M. / Warkocki, Z. / Taube, M. / Kolondra, A. / Czarnocki-Cieciura, M. / Nowak, E. / Labedzka-Dmoch, K. / Kawinska, A. / Piatkowski, J. / Golik, P. / Kozak, M. / Dziembowski, A. / Nowotny, M.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exoribonuclease II, mitochondrial
B: Suv3 helicase
C: RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)170,0643
Polymers170,0643
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-29 kcal/mol
Surface area62780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.550, 151.240, 284.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Exoribonuclease II, mitochondrial /


Mass: 94687.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 69 aminoacid N-terminal truncation was introduced in the full length protein
Source: (gene. exp.) Candida glabrata (fungus) / Gene: AO440_004157 / Production host: Escherichia coli (E. coli) / Variant (production host): RIL / References: UniProt: A0A0W0CXR7, UniProt: Q6FJE0*PLUS
#2: Protein Suv3 helicase


Mass: 73477.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 42 aminoacid N-terminal truncation and 14 aminoacid C-terminal truncation was introduced to the full length protein
Source: (gene. exp.) Candida glabrata (fungus) / Gene: SUV3, CAGL0L12386g / Production host: Escherichia coli (E. coli) / Variant (production host): RIL / References: UniProt: Q6FKD7
#3: RNA chain RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')


Mass: 1899.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNA molecule co-purified with the protein / Source: (natural) Escherichia coli (E. coli) / Variant: RIL

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium citrate tribasic (pH 7.0), 18% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.55→50.1 Å / Num. obs: 26391 / % possible obs: 95.4 % / Redundancy: 4.3 % / Rrim(I) all: 0.033 / Net I/σ(I): 27.4
Reflection shellResolution: 3.55→3.64 Å / Rrim(I) all: 0.225

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F3H, 3RC3

6f3h

3rc3


Resolution: 3.55→49.061 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3279 1318 4.99 %
Rwork0.2963 --
obs0.2978 26391 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.55→49.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7455 119 0 0 7574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077698
X-RAY DIFFRACTIONf_angle_d1.4410604
X-RAY DIFFRACTIONf_dihedral_angle_d12.4522243
X-RAY DIFFRACTIONf_chiral_restr0.0511319
X-RAY DIFFRACTIONf_plane_restr0.0081387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.69210.37531740.33962750X-RAY DIFFRACTION96
3.6921-3.86010.41761420.3412802X-RAY DIFFRACTION98
3.8601-4.06350.41281560.33922772X-RAY DIFFRACTION97
4.0635-4.3180.3211530.30562801X-RAY DIFFRACTION97
4.318-4.65110.33321510.28292741X-RAY DIFFRACTION95
4.6511-5.11870.36731360.28942846X-RAY DIFFRACTION97
5.1187-5.85840.35821260.33252756X-RAY DIFFRACTION94
5.8584-7.37690.35811390.32242806X-RAY DIFFRACTION95
7.3769-49.06560.2661410.25992799X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -3.4509 Å / Origin y: -51.2107 Å / Origin z: 31.8815 Å
111213212223313233
T1.1636 Å2-0.2299 Å20.0002 Å2-0.8711 Å20.0306 Å2--0.8244 Å2
L2.4411 °2-0.4305 °20.6347 °2-0.4778 °20.0311 °2--1.8229 °2
S0.1075 Å °-0.6573 Å °0.2265 Å °-0.1936 Å °-0.0294 Å °-0.1253 Å °-0.6751 Å °0.1983 Å °-0.074 Å °
Refinement TLS groupSelection details: all

+
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