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- PDB-4c92: Crystal structure of the yeast Lsm1-7 complex -

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Basic information

Entry
Database: PDB / ID: 4c92
TitleCrystal structure of the yeast Lsm1-7 complex
Components
  • (U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN ...) x 6
  • SM-LIKE PROTEIN LSM1
KeywordsTRANSCRIPTION / LSM1-7 / DECAPPING ACTIVATORS / MRNA DEGRADATION
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / RNA cap binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / U4/U6 snRNP / P-body assembly / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / RNA cap binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / U4/U6 snRNP / P-body assembly / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal snRNP assembly / U6 snRNA binding / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / rRNA processing / ribonucleoprotein complex / mRNA binding / chromatin binding / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
Sm-like protein Lsm1 / 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 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 ...Sm-like protein Lsm1 / 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 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / SH3 type barrels. - #100 / 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
U6 snRNA-associated Sm-like protein LSm2 / U6 snRNA-associated Sm-like protein LSm4 / U6 snRNA-associated Sm-like protein LSm5 / Sm-like protein LSm1 / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm3 / U6 snRNA-associated Sm-like protein LSm6
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsSharif, H. / Conti, E.
CitationJournal: Cell Rep. / Year: 2013
Title: Architecture of the Lsm1-7-Pat1 Complex: A Conserved Assembly in Eukaryotic Mrna Turnover
Authors: Sharif, H. / Conti, E.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SM-LIKE PROTEIN LSM1
B: U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2
C: U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3
D: 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


Theoretical massNumber of molelcules
Total (without water)85,4467
Polymers85,4467
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14410 Å2
ΔGint-80.7 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.796, 90.570, 68.462
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN ... , 6 types, 6 molecules BCDEFG

#2: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2 / SMALL NUCLEAR RIBONUCLEOPROTEIN D HOMOLOG SNP3 / LSM2


Mass: 12216.880 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P38203
#3: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3 / SMX4 PROTEIN / LSM3


Mass: 10039.262 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P57743
#4: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 / LSM4


Mass: 13035.543 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40070
#5: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5 / LSM5


Mass: 10432.954 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40089
#6: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6 / LSM6


Mass: 9406.579 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q06406
#7: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7 / 7


Mass: 13027.045 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53905

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Protein / Non-polymers , 2 types, 109 molecules A

#1: Protein SM-LIKE PROTEIN LSM1 / SPB8 PROTEIN / LSM1


Mass: 17287.596 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P47017
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.14 % / Description: MOLECULAR REPLACEMENT WITH CHIMERIC MODEL
Crystal growDetails: 100 MM MES PH 6.0, 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.998
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 2.3→95.57 Å / Num. obs: 62699 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 46.13 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2Y9A, 3BW1, 4EMK

2y9a
PDB Unreleased entry

3bw1

4emk


Resolution: 2.299→53.993 Å / SU ML: 0.39 / σ(F): 1.04 / Phase error: 32.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 3122 5 %
Rwork0.2109 --
obs0.2133 62641 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.19 Å2
Refinement stepCycle: LAST / Resolution: 2.299→53.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4891 0 0 108 4999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084947
X-RAY DIFFRACTIONf_angle_d1.2236680
X-RAY DIFFRACTIONf_dihedral_angle_d15.3841804
X-RAY DIFFRACTIONf_chiral_restr0.084797
X-RAY DIFFRACTIONf_plane_restr0.004854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2986-2.33450.34441210.32812289X-RAY DIFFRACTION82
2.3345-2.37280.35831430.32432777X-RAY DIFFRACTION97
2.3728-2.41370.42271410.33642687X-RAY DIFFRACTION98
2.4137-2.45760.37461490.33232744X-RAY DIFFRACTION96
2.4576-2.50480.38951400.3232657X-RAY DIFFRACTION96
2.5048-2.5560.37511490.32793X-RAY DIFFRACTION98
2.556-2.61150.36321440.29912744X-RAY DIFFRACTION99
2.6115-2.67230.34751440.28452781X-RAY DIFFRACTION99
2.6723-2.73910.35921460.27672779X-RAY DIFFRACTION99
2.7391-2.81320.29581460.25632779X-RAY DIFFRACTION99
2.8132-2.89590.31631420.24912745X-RAY DIFFRACTION99
2.8959-2.98940.31441460.24722781X-RAY DIFFRACTION98
2.9894-3.09620.31151460.23352733X-RAY DIFFRACTION98
3.0962-3.22020.2841440.21632719X-RAY DIFFRACTION97
3.2202-3.36670.2331400.20472678X-RAY DIFFRACTION97
3.3667-3.54420.26461470.19172758X-RAY DIFFRACTION97
3.5442-3.76620.24631390.18822716X-RAY DIFFRACTION97
3.7662-4.05690.21041340.18672714X-RAY DIFFRACTION97
4.0569-4.4650.21081380.17252627X-RAY DIFFRACTION94
4.465-5.11070.16861390.14532642X-RAY DIFFRACTION94
5.1107-6.43720.28971440.21832713X-RAY DIFFRACTION97
6.4372-54.00820.20061400.17672663X-RAY DIFFRACTION95

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