[English] 日本語
Yorodumi
- PDB-6ppq: Structure of S. pombe Lsm1-7 with RNA, polyuridine with 3' adenosine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ppq
TitleStructure of S. pombe Lsm1-7 with RNA, polyuridine with 3' adenosine
Components
  • (Probable U6 snRNA-associated Sm-like protein ...) x 2
  • (U6 snRNA-associated Sm-like protein ...) x 5
  • RNA (5'-R(*UP*UP*UP*UP*UP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / chromosome, telomeric repeat region / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA 3'-UTR AU-rich region binding / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex ...mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / chromosome, telomeric repeat region / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA 3'-UTR AU-rich region binding / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / P-body assembly / U2 snRNP / poly(U) RNA binding / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / telomerase holoenzyme complex assembly / nuclear-transcribed mRNA catabolic process / U5 snRNP / RNA folding / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / maturation of SSU-rRNA / spliceosomal complex / P-body / mRNA splicing, via spliceosome / RNA stem-loop binding / mRNA processing / rRNA processing / ribonucleoprotein complex / mRNA binding / chromatin binding / nucleolus / RNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Sm-like protein Lsm1 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Sm-like protein Lsm7 / U6 snRNA-associated Sm-like protein Lsm1/8 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG ...Sm-like protein Lsm1 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Sm-like protein Lsm7 / U6 snRNA-associated Sm-like protein Lsm1/8 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / LSM complex subunit lsm4 / LSM complex subunit lsm5 / LSM complex subunit lsm7 / LSM complex subunit lsm2 / LSM1-LSM7 complex subunit lsm1 / LSM complex subunit lsm6 / LSM complex subunit lsm3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsMontemayor, E.J. / Butcher, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118131 United States
CitationJournal: Rna / Year: 2020
Title: Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes.
Authors: Montemayor, E.J. / Virta, J.M. / Hayes, S.M. / Nomura, Y. / Brow, D.A. / Butcher, S.E.
History
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 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: U6 snRNA-associated Sm-like protein LSm1
B: U6 snRNA-associated Sm-like protein LSm2
C: Probable U6 snRNA-associated Sm-like protein LSm3
D: Probable U6 snRNA-associated Sm-like protein LSm4
E: U6 snRNA-associated Sm-like protein LSm5
F: U6 snRNA-associated Sm-like protein LSm6
G: U6 snRNA-associated Sm-like protein LSm7
H: RNA (5'-R(*UP*UP*UP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)79,0718
Polymers79,0718
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint-81 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.857, 68.857, 296.297
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

-
U6 snRNA-associated Sm-like protein ... , 5 types, 5 molecules ABEFG

#1: Protein U6 snRNA-associated Sm-like protein LSm1


Mass: 9754.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: lsm1, SPBC3D6.08c / Production host: Escherichia coli (E. coli) / References: UniProt: P87173
#2: Protein U6 snRNA-associated Sm-like protein LSm2


Mass: 11003.798 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: lsm2, SPCC1620.01c / Production host: Escherichia coli (E. coli) / References: UniProt: O94408
#5: Protein U6 snRNA-associated Sm-like protein LSm5


Mass: 8860.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: lsm5, SPBC20F10.09 / Production host: Escherichia coli (E. coli) / References: UniProt: O42978
#6: Protein U6 snRNA-associated Sm-like protein LSm6


Mass: 8489.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: lsm6, SPAC2F3.17c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UUI1
#7: Protein U6 snRNA-associated Sm-like protein LSm7


Mass: 13317.060 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: lsm7, SPCC285.12 / Production host: Escherichia coli (E. coli) / References: UniProt: O74499

-
Probable U6 snRNA-associated Sm-like protein ... , 2 types, 2 molecules CD

#3: Protein Probable U6 snRNA-associated Sm-like protein LSm3


Mass: 10824.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: lsm3, SPBC9B6.05c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y7M4
#4: Protein Probable U6 snRNA-associated Sm-like protein LSm4


Mass: 15007.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: lsm4, SPBC30D10.06 / Production host: Escherichia coli (E. coli) / References: UniProt: O14352

-
RNA chain / Non-polymers , 2 types, 303 molecules H

#8: RNA chain RNA (5'-R(*UP*UP*UP*UP*UP*A)-3')


Mass: 1815.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium tartrate, 20 mM sodium oxamate, 100 mM sodium HEPES base, 100 mM MOPS acid, 10 % PEG 8,000, 20 % ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.976177 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976177 Å / Relative weight: 1
ReflectionResolution: 1.81→98.8 Å / Num. obs: 75844 / % possible obs: 100 % / Redundancy: 31.4 % / Net I/σ(I): 15.4
Reflection shellResolution: 1.81→1.88 Å / Num. unique obs: 4347

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→34.5 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs75844 100 %
Refinement stepCycle: LAST / Resolution: 1.81→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 102 0 302 4669

+
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