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- PDB-4emk: Crystal structure of SpLsm5/6/7 -

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Basic information

Entry
Database: PDB / ID: 4emk
TitleCrystal structure of SpLsm5/6/7
Components
  • U6 snRNA-associated Sm-like protein LSm5
  • U6 snRNA-associated Sm-like protein LSm6
  • U6 snRNA-associated Sm-like protein LSm7
KeywordsRNA BINDING PROTEIN / Sm fold / mRNA decay and pre-mRNA splicing / Lsm proteins
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / Lsm1-7-Pat1 complex / U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2 snRNP / poly(U) RNA binding ...mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / Lsm1-7-Pat1 complex / U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2 snRNP / poly(U) RNA binding / U2-type prespliceosome / tRNA processing / telomerase holoenzyme complex assembly / nuclear-transcribed mRNA catabolic process / U5 snRNP / U2 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / maturation of SSU-rRNA / spliceosomal complex / P-body / mRNA splicing, via spliceosome / rRNA processing / nucleolus / RNA binding / nucleus / cytosol
Similarity search - Function
Sm-like protein Lsm7 / Sm-like protein LSm5 / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. ...Sm-like protein Lsm7 / Sm-like protein LSm5 / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / 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
LSM complex subunit lsm5 / LSM complex subunit lsm7 / LSM complex subunit lsm6
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJiang, S.M. / Wu, D.H. / Song, H.W.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structures of Lsm3, Lsm4 and Lsm5/6/7 from Schizosaccharomyces pombe.
Authors: Wu, D.H. / Jiang, S.M. / Bowler, M.W. / Song, H.W.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U6 snRNA-associated Sm-like protein LSm5
B: U6 snRNA-associated Sm-like protein LSm6
C: U6 snRNA-associated Sm-like protein LSm7


Theoretical massNumber of molelcules
Total (without water)31,8753
Polymers31,8753
Non-polymers00
Water1,27971
1
A: U6 snRNA-associated Sm-like protein LSm5
B: U6 snRNA-associated Sm-like protein LSm6
C: U6 snRNA-associated Sm-like protein LSm7

A: U6 snRNA-associated Sm-like protein LSm5
B: U6 snRNA-associated Sm-like protein LSm6
C: U6 snRNA-associated Sm-like protein LSm7


Theoretical massNumber of molelcules
Total (without water)63,7516
Polymers63,7516
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9310 Å2
ΔGint-42 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.430, 69.430, 172.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein U6 snRNA-associated Sm-like protein LSm5


Mass: 10807.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: lsm5, SPBC20F10.09 / Production host: Escherichia coli (E. coli) / References: UniProt: O42978
#2: Protein U6 snRNA-associated Sm-like protein LSm6


Mass: 8439.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: lsm6, SPAC2F3.17c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UUI1
#3: Protein U6 snRNA-associated Sm-like protein LSm7


Mass: 12628.864 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: lsm7, SPCC285.12 / Production host: Escherichia coli (E. coli) / References: UniProt: O74499
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, pH 6.5, 0.1M MgCl2, 32% polyethylene glycol (PEG) 400, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→86.16 Å / Num. all: 19618 / Num. obs: 19618 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.42 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→54.053 Å / SU ML: 0.31 / σ(F): 1 / Phase error: 24.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 952 5.17 %Random
Rwork0.2311 ---
all0.2323 18409 --
obs0.2323 18409 94.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.62 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7754 Å20 Å2-0 Å2
2--4.7754 Å20 Å2
3----9.5508 Å2
Refinement stepCycle: LAST / Resolution: 2.3→54.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 0 71 1650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091595
X-RAY DIFFRACTIONf_angle_d1.2472148
X-RAY DIFFRACTIONf_dihedral_angle_d17.424594
X-RAY DIFFRACTIONf_chiral_restr0.078256
X-RAY DIFFRACTIONf_plane_restr0.004272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.42130.3588990.2862192775
2.4213-2.5730.33321140.2548232789
2.573-2.77170.28381470.2351250797
2.7717-3.05060.31171440.2343258799
3.0506-3.49190.22231480.2061261699
3.4919-4.39910.22971560.19522647100
4.3991-54.0680.23581440.24832846100

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