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- PDB-6ppv: Structure of S. pombe Lsm1-7 with RNA, polyuridine with 3' guanosine -

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Basic information

Entry
Database: PDB / ID: 6ppv
TitleStructure of S. pombe Lsm1-7 with RNA, polyuridine with 3' guanosine
Components
  • (Probable U6 snRNA-associated Sm-like protein ...) x 2
  • (U6 snRNA-associated Sm-like protein ...) x 5
  • RNA (5'-R(*AP*UP*UP*UP*UP*G)-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 / cytosol / cytoplasm
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: 2.05 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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(*AP*UP*UP*UP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)78,2828
Polymers78,2828
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-85 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.023, 69.023, 296.068
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

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Components

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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: 12488.179 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

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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

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RNA chain / Non-polymers , 2 types, 191 molecules H

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


Mass: 1854.117 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.: 190 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.05→98.7 Å / Num. obs: 52874 / % possible obs: 100 % / Redundancy: 21.1 % / Biso Wilson estimate: 45.4 Å2 / Net I/σ(I): 11.6
Reflection shellResolution: 2.05→2.11 Å / Num. unique obs: 4047

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→42.07 Å / SU ML: 0.3426 / Cross valid method: FREE R-VALUE / σ(F): 0.42 / Phase error: 29.1337
RfactorNum. reflection% reflection
Rfree0.2446 3798 3.84 %
Rwork0.2086 --
obs0.21 52767 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.94 Å2
Refinement stepCycle: LAST / Resolution: 2.05→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 122 0 190 4577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544456
X-RAY DIFFRACTIONf_angle_d0.86066053
X-RAY DIFFRACTIONf_chiral_restr0.0542728
X-RAY DIFFRACTIONf_plane_restr0.0042750
X-RAY DIFFRACTIONf_dihedral_angle_d17.25722687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.3661360.36653569X-RAY DIFFRACTION100
2.08-2.10.3931360.34873522X-RAY DIFFRACTION99.97
2.1-2.130.39271340.34533475X-RAY DIFFRACTION99.92
2.13-2.160.39991440.33393607X-RAY DIFFRACTION99.97
2.16-2.190.36691360.33513439X-RAY DIFFRACTION100
2.19-2.230.38241400.30813629X-RAY DIFFRACTION99.95
2.23-2.270.35431360.30293416X-RAY DIFFRACTION99.97
2.27-2.30.33541410.29283672X-RAY DIFFRACTION100
2.3-2.350.31911460.26973446X-RAY DIFFRACTION100
2.35-2.390.29941360.26763547X-RAY DIFFRACTION99.97
2.39-2.440.2931340.25193501X-RAY DIFFRACTION100
2.44-2.490.28131440.24973534X-RAY DIFFRACTION100
2.49-2.550.35321420.2613565X-RAY DIFFRACTION100
2.55-2.620.37891380.24643478X-RAY DIFFRACTION100
2.62-2.690.28761340.24363513X-RAY DIFFRACTION100
2.69-2.770.31521540.23333584X-RAY DIFFRACTION99.95
2.77-2.850.26851420.21843508X-RAY DIFFRACTION100
2.85-2.960.24471380.21653472X-RAY DIFFRACTION99.97
2.96-3.070.2411450.21983533X-RAY DIFFRACTION100
3.07-3.210.25051480.21553478X-RAY DIFFRACTION99.97
3.21-3.380.24161380.20753552X-RAY DIFFRACTION100
3.38-3.60.25531390.19143531X-RAY DIFFRACTION99.97
3.6-3.870.17961420.18913552X-RAY DIFFRACTION99.86
3.87-4.260.22261420.1733507X-RAY DIFFRACTION99.84
4.26-4.880.17481560.1443498X-RAY DIFFRACTION99.65
4.88-6.140.25131400.18243515X-RAY DIFFRACTION99.95
6.14-42.070.18371370.19293528X-RAY DIFFRACTION99.62

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