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- PDB-6ppp: Structure of S. pombe Lsm2-8 with processed U6 snRNA -

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Basic information

Entry
Database: PDB / ID: 6ppp
TitleStructure of S. pombe Lsm2-8 with processed U6 snRNA
Components
  • (Probable U6 snRNA-associated Sm-like protein ...) x 2
  • (U6 snRNA-associated Sm-like protein ...) x 5
  • Mimic of processed U6 snRNA
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 / RNA metabolic process / Lsm1-7-Pat1 complex / U6 snRNP / P-body assembly / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / mRNA cis splicing, via spliceosome ...mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / chromosome, telomeric repeat region / RNA metabolic process / Lsm1-7-Pat1 complex / U6 snRNP / P-body assembly / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / telomerase holoenzyme complex / U2 snRNP / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / telomerase holoenzyme complex assembly / RNA folding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / chromatin binding / nucleolus / RNA binding / nucleus / cytosol
Similarity search - Function
Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein Lsm1/8 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Sm-like protein Lsm7 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / Sm-like protein Lsm7/SmG / SH3 type barrels. - #100 ...Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein Lsm1/8 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Sm-like protein Lsm7 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / Sm-like protein Lsm7/SmG / SH3 type barrels. - #100 / 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 / Probable U6 snRNA-associated Sm-like protein LSm4 / U6 snRNA-associated Sm-like protein LSm5 / U6 snRNA-associated Sm-like protein LSm8 / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm2 / U6 snRNA-associated Sm-like protein LSm6 / Probable U6 snRNA-associated Sm-like protein LSm3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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 1.2Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mimic of processed U6 snRNA
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: U6 snRNA-associated Sm-like protein LSm8
I: Mimic of processed U6 snRNA
J: U6 snRNA-associated Sm-like protein LSm2
K: Probable U6 snRNA-associated Sm-like protein LSm3
L: Probable U6 snRNA-associated Sm-like protein LSm4
M: U6 snRNA-associated Sm-like protein LSm5
N: U6 snRNA-associated Sm-like protein LSm6
O: U6 snRNA-associated Sm-like protein LSm7
P: U6 snRNA-associated Sm-like protein LSm8


Theoretical massNumber of molelcules
Total (without water)159,77816
Polymers159,77816
Non-polymers00
Water46826
1
A: Mimic of processed U6 snRNA
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: U6 snRNA-associated Sm-like protein LSm8


Theoretical massNumber of molelcules
Total (without water)79,8898
Polymers79,8898
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Mimic of processed U6 snRNA
J: U6 snRNA-associated Sm-like protein LSm2
K: Probable U6 snRNA-associated Sm-like protein LSm3
L: Probable U6 snRNA-associated Sm-like protein LSm4
M: U6 snRNA-associated Sm-like protein LSm5
N: U6 snRNA-associated Sm-like protein LSm6
O: U6 snRNA-associated Sm-like protein LSm7
P: U6 snRNA-associated Sm-like protein LSm8


Theoretical massNumber of molelcules
Total (without water)79,8898
Polymers79,8898
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.260, 139.690, 153.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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U6 snRNA-associated Sm-like protein ... , 5 types, 10 molecules BJEMFNGOHP

#2: Protein U6 snRNA-associated Sm-like protein LSm2


Mass: 11003.798 Da / Num. of mol.: 2
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.: 2
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.: 2
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.: 2
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
#8: Protein U6 snRNA-associated Sm-like protein LSm8


Mass: 10572.005 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: lsm8, SPCC1840.10 / Production host: Escherichia coli (E. coli) / References: UniProt: O74483

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Probable U6 snRNA-associated Sm-like protein ... , 2 types, 4 molecules CKDL

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


Mass: 10824.278 Da / Num. of mol.: 2
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.: 2
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

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RNA chain / Non-polymers , 2 types, 28 molecules AI

#1: RNA chain Mimic of processed U6 snRNA


Mass: 1815.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 50 mM KCl 50 mM HEPES pH 7 Pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078123 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078123 Å / Relative weight: 1
ReflectionResolution: 2.33→78 Å / Num. obs: 28712 / % possible obs: 43.7 % / Redundancy: 86.9 % / Net I/σ(I): 16
Reflection shellResolution: 2.33→2.73 Å / Num. unique obs: 1433

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EMG, 4EMH, 4EMK, 4C92, 4M7D

4emg

4emh

4emk

4c92

4m7d


Resolution: 2.33→51.7 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs28712 43.7 %
Refinement stepCycle: LAST / Resolution: 2.33→51.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8615 200 0 26 8841

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