[English] 日本語
Yorodumi
- PDB-6ygu: Crystal structure of the minimal Mtr4-Red1 complex (single chain)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ygu
TitleCrystal structure of the minimal Mtr4-Red1 complex (single chain) from Chaetomium thermophilum
Components
  • ATP dependent RNA helicase (Dob1)-like protein
  • Red1
KeywordsRNA BINDING PROTEIN / ncRNA degradation / MTREC / nuclear exosome
Function / homology
Function and homology information


exosome (RNase complex) / RNA catabolic process / RNA helicase activity / hydrolase activity / RNA binding / ATP binding / nucleus / metal ion binding
Similarity search - Function
NURS complex subunit red1 / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : ...NURS complex subunit red1 / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / ATP dependent RNA helicase (Dob1)-like protein / Zinc-finger domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsDobrev, N. / Ahmed, Y.L. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Nat Commun / Year: 2021
Title: The zinc-finger protein Red1 orchestrates MTREC submodules and binds the Mtl1 helicase arch domain.
Authors: Dobrev, N. / Ahmed, Y.L. / Sivadas, A. / Soni, K. / Fischer, T. / Sinning, I.
History
DepositionMar 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP dependent RNA helicase (Dob1)-like protein
B: Red1
C: ATP dependent RNA helicase (Dob1)-like protein
D: Red1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,27816
Polymers69,5334
Non-polymers74512
Water3,243180
1
A: ATP dependent RNA helicase (Dob1)-like protein
B: Red1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,38412
Polymers34,7662
Non-polymers61810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATP dependent RNA helicase (Dob1)-like protein
D: Red1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8944
Polymers34,7662
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.979, 88.906, 168.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein ATP dependent RNA helicase (Dob1)-like protein


Mass: 24791.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0001850 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0RZ64
#2: Protein Red1


Mass: 9975.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0014920 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0S1V1

-
Non-polymers , 4 types, 192 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Magnesium Acetate 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2741 Å / Relative weight: 1
ReflectionResolution: 1.99→47.46 Å / Num. obs: 47338 / % possible obs: 99.91 % / Redundancy: 13 % / Biso Wilson estimate: 38.87 Å2 / Rmerge(I) obs: 0.1033 / Net I/σ(I): 13.45
Reflection shellResolution: 1.99→2.061 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.332 / Mean I/σ(I) obs: 1.55 / Num. unique obs: 4660 / % possible all: 99.79

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.99→47.458 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.22 / Phase error: 29.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 4511 5.05 %
Rwork0.2045 --
obs0.2068 89392 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→47.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 42 180 4701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134633
X-RAY DIFFRACTIONf_angle_d1.3176255
X-RAY DIFFRACTIONf_dihedral_angle_d11.1173263
X-RAY DIFFRACTIONf_chiral_restr0.069660
X-RAY DIFFRACTIONf_plane_restr0.009826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.01260.40261630.34082819X-RAY DIFFRACTION100
2.0126-2.03630.35211330.33082873X-RAY DIFFRACTION100
2.0363-2.06110.37721630.31862795X-RAY DIFFRACTION100
2.0611-2.08720.39781420.30962803X-RAY DIFFRACTION100
2.0872-2.11470.36141710.28692829X-RAY DIFFRACTION100
2.1147-2.14370.40221750.28552833X-RAY DIFFRACTION100
2.1437-2.17430.32931480.26852784X-RAY DIFFRACTION100
2.1743-2.20670.29041230.24962842X-RAY DIFFRACTION100
2.2067-2.24120.32371550.2582858X-RAY DIFFRACTION100
2.2412-2.2780.3921640.24422812X-RAY DIFFRACTION100
2.278-2.31720.25791590.24482798X-RAY DIFFRACTION100
2.3172-2.35940.31291180.24412895X-RAY DIFFRACTION100
2.3594-2.40480.31681660.23842760X-RAY DIFFRACTION100
2.4048-2.45380.29211690.23632829X-RAY DIFFRACTION100
2.4538-2.50720.26991500.22932881X-RAY DIFFRACTION100
2.5072-2.56550.2911510.21742789X-RAY DIFFRACTION100
2.5655-2.62970.29781500.22292869X-RAY DIFFRACTION100
2.6297-2.70080.30081610.22682802X-RAY DIFFRACTION100
2.7008-2.78020.31081290.22862838X-RAY DIFFRACTION100
2.7802-2.870.2821710.22682810X-RAY DIFFRACTION100
2.87-2.97250.23791410.21962855X-RAY DIFFRACTION100
2.9725-3.09150.29091610.2242794X-RAY DIFFRACTION100
3.0915-3.23220.25771620.2192867X-RAY DIFFRACTION100
3.2322-3.40250.2421300.22672815X-RAY DIFFRACTION100
3.4025-3.61560.21531440.20472813X-RAY DIFFRACTION100
3.6156-3.89470.19831480.18452846X-RAY DIFFRACTION100
3.8947-4.28640.17091390.1642832X-RAY DIFFRACTION100
4.2864-4.90610.21231340.15472877X-RAY DIFFRACTION100
4.9061-6.1790.24981320.17552842X-RAY DIFFRACTION100
6.179-47.47120.21751590.16312821X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.3685 Å / Origin y: 15.5537 Å / Origin z: 107.7067 Å
111213212223313233
T0.2245 Å2-0.0358 Å2-0.0123 Å2-0.3152 Å20.0262 Å2--0.2878 Å2
L0.3009 °2-0.2976 °20.1033 °2-1.0142 °2-0.1945 °2--0.5757 °2
S0.0114 Å °-0.0913 Å °-0.0287 Å °0.0048 Å °0.0364 Å °0.0648 Å °0.0174 Å °-0.0658 Å °0.0005 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