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- PDB-3bw1: Crystal structure of homomeric yeast Lsm3 exhibiting novel octame... -

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Basic information

Entry
Database: PDB / ID: 3bw1
TitleCrystal structure of homomeric yeast Lsm3 exhibiting novel octameric ring organisation
ComponentsU6 snRNA-associated Sm-like protein LSm3
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / SM-LIKE PROTEIN / SM PROTEIN / RING / HOMOMERIC / OCTAMER / mRNA processing / mRNA splicing / Nucleus / Ribonucleoprotein / rRNA processing / tRNA processing
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / U4/U6 snRNP / P-body assembly / sno(s)RNA-containing ribonucleoprotein complex / tRNA processing / precatalytic spliceosome / U4/U6 x U5 tri-snRNP complex ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / U4/U6 snRNP / P-body assembly / sno(s)RNA-containing ribonucleoprotein complex / tRNA processing / precatalytic spliceosome / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / 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 LSm3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNaidoo, N. / Harrop, S.J. / Curmi, P.M.G. / Mabbutt, B.C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of Lsm3 octamer from Saccharomyces cerevisiae: implications for Lsm ring organisation and recruitment
Authors: Naidoo, N. / Harrop, S.J. / Sobti, M. / Haynes, P.A. / Szymczyna, B.R. / Williamson, J.R. / Curmi, P.M.G. / Mabbutt, B.C.
History
DepositionJan 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all ..._reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 LSm3
B: U6 snRNA-associated Sm-like protein LSm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5677
Polymers21,9992
Non-polymers5695
Water362
1
A: U6 snRNA-associated Sm-like protein LSm3
B: U6 snRNA-associated Sm-like protein LSm3
hetero molecules

A: U6 snRNA-associated Sm-like protein LSm3
B: U6 snRNA-associated Sm-like protein LSm3
hetero molecules

A: U6 snRNA-associated Sm-like protein LSm3
B: U6 snRNA-associated Sm-like protein LSm3
hetero molecules

A: U6 snRNA-associated Sm-like protein LSm3
B: U6 snRNA-associated Sm-like protein LSm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,27028
Polymers87,9958
Non-polymers2,27520
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area21230 Å2
ΔGint-296.2 kcal/mol
Surface area38540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.743, 83.743, 141.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 1 - 80 / Label seq-ID: 8 - 87

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein U6 snRNA-associated Sm-like protein LSm3 / SmX4 protein


Mass: 10999.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMX4 / Plasmid: pETMCSIII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P57743
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.75M lithium sulfate, 8% (v/v) 2-methyl-2,4-pentanediol, 0.1M imidazole (pH 7.0), 10mM uridine-5-monophosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2005
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.45→36.25 Å / Num. all: 9583 / Num. obs: 9073 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 71.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 23.7
Reflection shellResolution: 2.45→2.57 Å / Rmerge(I) obs: 1.405 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1169 / % possible all: 83.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I81

1i81


Resolution: 2.5→24.04 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 23.823 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24296 429 4.7 %RANDOM
Rwork0.21564 ---
all0.21694 9073 --
obs0.21694 8603 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.78 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 37 2 1407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221424
X-RAY DIFFRACTIONr_angle_refined_deg2.1252.0031931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5035170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87824.17967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.43815257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6881512
X-RAY DIFFRACTIONr_chiral_restr0.1290.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021023
X-RAY DIFFRACTIONr_nbd_refined0.2540.2508
X-RAY DIFFRACTIONr_nbtor_refined0.3240.2958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.26
X-RAY DIFFRACTIONr_mcbond_it0.7981.5879
X-RAY DIFFRACTIONr_mcangle_it1.39221400
X-RAY DIFFRACTIONr_scbond_it2.2763585
X-RAY DIFFRACTIONr_scangle_it3.4164.5530
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 626 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.070.05
tight thermal0.130.5
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 28 -
Rwork0.393 601 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.42830.02075.11272.2544-0.44057.23720.3462-0.880.27470.68130.0188-0.0542-0.0326-0.1213-0.3650.0965-0.02440.073-0.2593-0.197-0.05510.599223.252419.8099
26.8008-4.11282.19447.5471-2.82269.80140.0506-0.81210.05910.96350.3494-0.3299-0.08890.0165-0.4-0.0952-0.1776-0.0934-0.0972-0.1629-0.060717.004316.075519.8517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 808 - 87
2X-RAY DIFFRACTION2BB1 - 808 - 87

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