[English] 日本語
Yorodumi
- PDB-6fpq: Structure of S. pombe Mmi1 in complex with 7-mer RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fpq
TitleStructure of S. pombe Mmi1 in complex with 7-mer RNA
Components
  • RNA (5'-R(*UP*UP*AP*AP*AP*CP*C)-3')
  • YTH domain-containing protein mmi1
KeywordsRNA BINDING PROTEIN / Meiosis mRNA decay
Function / homology
Function and homology information


: / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / nuclear RNA surveillance / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / heterochromatin island ...: / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / nuclear RNA surveillance / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / heterochromatin island / nuclear mRNA surveillance of mRNA 3'-end processing / lncRNA catabolic process / CCR4-NOT complex binding / protein-RNA adaptor activity / regulatory ncRNA 3'-end processing / N6-methyladenosine-containing RNA reader activity / pre-mRNA binding / lncRNA binding / mRNA destabilization / pre-mRNA intronic binding / mRNA binding / chromatin / DNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
RNA / RNA binding exosome specificity factor Mmi1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.42 Å
AuthorsStowell, J.A.W. / Hill, C.H. / Yu, M. / Wagstaff, J.L. / McLaughlin, S.H. / Freund, S.M.V. / Passmore, L.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105192715 United Kingdom
European Research Council261151
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding.
Authors: Stowell, J.A.W. / Wagstaff, J.L. / Hill, C.H. / Yu, M. / McLaughlin, S.H. / Freund, S.M.V. / Passmore, L.A.
History
DepositionFeb 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 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: YTH domain-containing protein mmi1
B: RNA (5'-R(*UP*UP*AP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9614
Polymers23,7252
Non-polymers2362
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Consistent with monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint3 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.406, 77.406, 66.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein YTH domain-containing protein mmi1 / Meiotic mRNA interception protein 1


Mass: 21559.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: mmi1, SPCC736.12c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O74958
#2: RNA chain RNA (5'-R(*UP*UP*AP*AP*AP*CP*C)-3')


Mass: 2165.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% (v/v) Ethanol, 10mM Magnesium sulfate, 0.1M Tris pH 8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 25, 2016
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.42→47.1 Å / Num. obs: 42567 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.6
Reflection shellResolution: 1.42→1.47 Å / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4135 / CC1/2: 0.548 / % possible all: 99.6

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 1.42→47.1 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.75
Details: TLS groups used: tls = chain 'A' and (resid 12 through 46 ) tls = chain 'A' and (resid 47 through 185 ) tls = chain 'B' and (resid -2 through 5 )
RfactorNum. reflection% reflection
Rfree0.1678 2146 5.05 %
Rwork0.1429 --
obs0.1442 42527 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.42→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 143 16 229 1768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171735
X-RAY DIFFRACTIONf_angle_d1.5912388
X-RAY DIFFRACTIONf_dihedral_angle_d25.566680
X-RAY DIFFRACTIONf_chiral_restr0.119258
X-RAY DIFFRACTIONf_plane_restr0.009289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.45310.29471330.27572672X-RAY DIFFRACTION99
1.4531-1.48940.23641550.22912669X-RAY DIFFRACTION100
1.4894-1.52970.22991540.19492646X-RAY DIFFRACTION100
1.5297-1.57470.18761370.18242714X-RAY DIFFRACTION100
1.5747-1.62550.16381280.16762690X-RAY DIFFRACTION100
1.6255-1.68360.18051310.15492698X-RAY DIFFRACTION100
1.6836-1.7510.18371380.14742691X-RAY DIFFRACTION100
1.751-1.83070.15951380.14442693X-RAY DIFFRACTION100
1.8307-1.92720.15481440.1352674X-RAY DIFFRACTION100
1.9272-2.0480.15521470.13652715X-RAY DIFFRACTION100
2.048-2.20610.15671370.13132674X-RAY DIFFRACTION100
2.2061-2.42810.17371610.1332682X-RAY DIFFRACTION100
2.4281-2.77940.14991410.13612701X-RAY DIFFRACTION100
2.7794-3.50160.151500.13182719X-RAY DIFFRACTION100
3.5016-47.10.1681520.1292743X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9073-0.6016-0.43191.6427-1.33072.8338-0.0794-0.2336-0.3737-0.0046-0.0975-0.24090.16650.37970.13870.15260.01280.02110.1760.0340.20862.254624.6763-53.7168
20.6866-0.003-0.13490.40650.16621.3586-0.00810.01570.0235-0.028-0.02010.0229-0.063-0.06730.02860.1084-0.008-0.0030.10650.00130.1142-12.267440.6965-56.2785
31.62780.0126-0.45121.08060.681.8442-0.1429-0.0873-0.49680.2025-0.01970.26160.2665-0.03720.08380.1943-0.03470.02390.15470.0160.2155-15.132524.7413-48.8908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 185 )
3X-RAY DIFFRACTION3chain 'B' and (resid -2 through 5 )

+
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://pdbjlvh1.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