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- PDB-4m75: Crystal structure of Lsm1-7 complex -

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Basic information

Entry
Database: PDB / ID: 4m75
TitleCrystal structure of Lsm1-7 complex
Components(U6 snRNA-associated Sm-like protein ...) x 7
KeywordsRNA BINDING PROTEIN / Sm Like Protein / RNA splicing / STRUCTURAL PROTEIN
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: 2.95 Å
AuthorsZhou, L. / Hang, J. / Zhou, Y. / Wan, R. / Lu, G. / Yan, C. / Shi, Y.
CitationJournal: Nature / Year: 2014
Title: Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA.
Authors: Zhou, L. / Hang, J. / Zhou, Y. / Wan, R. / Lu, G. / Yin, P. / Yan, C. / Shi, Y.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Sep 20, 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_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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 Lsm1
B: U6 snRNA-associated Sm-like protein Lsm2
C: U6 snRNA-associated Sm-like protein Lsm3
D: U6 snRNA-associated Sm-like protein Lsm6
E: U6 snRNA-associated Sm-like protein Lsm5
F: U6 snRNA-associated Sm-like protein Lsm7
G: U6 snRNA-associated Sm-like protein Lsm4
H: U6 snRNA-associated Sm-like protein Lsm1
I: U6 snRNA-associated Sm-like protein Lsm2
J: U6 snRNA-associated Sm-like protein Lsm3
K: U6 snRNA-associated Sm-like protein Lsm6
L: U6 snRNA-associated Sm-like protein Lsm5
M: U6 snRNA-associated Sm-like protein Lsm7
N: U6 snRNA-associated Sm-like protein Lsm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,76716
Polymers172,69614
Non-polymers712
Water0
1
A: U6 snRNA-associated 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 Lsm6
E: U6 snRNA-associated Sm-like protein Lsm5
F: U6 snRNA-associated Sm-like protein Lsm7
G: U6 snRNA-associated Sm-like protein Lsm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4199
Polymers86,3487
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint-103 kcal/mol
Surface area27480 Å2
MethodPISA
2
H: U6 snRNA-associated Sm-like protein Lsm1
I: U6 snRNA-associated Sm-like protein Lsm2
J: U6 snRNA-associated Sm-like protein Lsm3
K: U6 snRNA-associated Sm-like protein Lsm6
L: U6 snRNA-associated Sm-like protein Lsm5
M: U6 snRNA-associated Sm-like protein Lsm7
N: U6 snRNA-associated Sm-like protein Lsm4


Theoretical massNumber of molelcules
Total (without water)86,3487
Polymers86,3487
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12990 Å2
ΔGint-76 kcal/mol
Surface area26300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.672, 67.835, 98.235
Angle α, β, γ (deg.)93.14, 108.21, 116.30
Int Tables number1
Space group name H-MP1

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Components

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U6 snRNA-associated Sm-like protein ... , 7 types, 14 molecules AHBICJDKELFMGN

#1: Protein U6 snRNA-associated Sm-like protein Lsm1


Mass: 17473.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM1, SPB8, YJL124C, J0714 / Production host: Escherichia coli (E. coli) / References: UniProt: P47017
#2: Protein U6 snRNA-associated Sm-like protein Lsm2


Mass: 11302.508 Da / Num. of mol.: 2 / Mutation: C45S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM2, SMX5, SNP3, YBL026W, YBL0425 / Production host: Escherichia coli (E. coli) / References: UniProt: P38203
#3: Protein U6 snRNA-associated Sm-like protein Lsm3


Mass: 10100.921 Da / Num. of mol.: 2 / Mutation: C37S,C63S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM3, SMX4, USS2, YLR438C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P57743
#4: Protein U6 snRNA-associated Sm-like protein Lsm6


Mass: 9547.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / References: UniProt: Q06406
#5: Protein U6 snRNA-associated Sm-like protein Lsm5


Mass: 10573.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM5, YER146W / Production host: Escherichia coli (E. coli) / References: UniProt: P40089
#6: Protein U6 snRNA-associated Sm-like protein Lsm7


Mass: 13261.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / References: UniProt: P53905
#7: Protein U6 snRNA-associated Sm-like protein Lsm4


Mass: 14088.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / References: UniProt: P40070

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Non-polymers , 1 types, 2 molecules

#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES 6.5, 25% PEG600, 20mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.95→3.06 Å / % possible all: 98.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I81

1i81


Resolution: 2.95→38.66 Å / SU ML: 0.56 / σ(F): 0.89 / Phase error: 31.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.291 2954 5.08 %
Rwork0.266 --
obs0.267 58102 96.7 %
all-60091 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.09 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.3686 Å29.7927 Å22.5732 Å2
2--3.7437 Å23.2479 Å2
3---15.6374 Å2
Refinement stepCycle: LAST / Resolution: 2.95→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9317 0 2 0 9319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0199438
X-RAY DIFFRACTIONf_angle_d1.66512719
X-RAY DIFFRACTIONf_dihedral_angle_d22.493466
X-RAY DIFFRACTIONf_chiral_restr0.091511
X-RAY DIFFRACTIONf_plane_restr0.011608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.99840.4541110.40122600X-RAY DIFFRACTION95
2.9984-3.05010.33841550.37272642X-RAY DIFFRACTION97
3.0501-3.10550.47031420.3592643X-RAY DIFFRACTION98
3.1055-3.16520.35081450.36732692X-RAY DIFFRACTION98
3.1652-3.22980.46041370.36652687X-RAY DIFFRACTION98
3.2298-3.30.3565980.34052629X-RAY DIFFRACTION97
3.3-3.37670.41511560.322697X-RAY DIFFRACTION98
3.3767-3.46110.28631400.29382617X-RAY DIFFRACTION98
3.4611-3.55460.32831520.27432721X-RAY DIFFRACTION98
3.5546-3.65910.24061540.27422586X-RAY DIFFRACTION98
3.6591-3.77720.27441470.27742690X-RAY DIFFRACTION98
3.7772-3.9120.27041370.26492637X-RAY DIFFRACTION98
3.912-4.06850.29121610.25542621X-RAY DIFFRACTION98
4.0685-4.25340.29281630.24472628X-RAY DIFFRACTION97
4.2534-4.47740.20431460.212642X-RAY DIFFRACTION96
4.4774-4.75740.23781220.1852609X-RAY DIFFRACTION95
4.7574-5.1240.22611220.20612631X-RAY DIFFRACTION96
5.124-5.63820.28691530.28332560X-RAY DIFFRACTION96
5.6382-6.45080.37171230.30682646X-RAY DIFFRACTION96
6.4508-8.1150.27761580.27262497X-RAY DIFFRACTION93
8.115-38.66090.27351320.24512473X-RAY DIFFRACTION91
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)
12.4836-0.4018-0.55351.56140.18412.5784-0.11420.22850.6353-0.119-0.3777-0.588-0.74560.007-0.2344-0.1446-0.15220.24120.0690.13370.1154-30.836336.26730.6227
25.9897-2.18310.27126.6577-0.59867.1871-0.0051-0.68460.47040.54520.1246-0.4875-0.30860.24910.06010.21-0.0475-0.07740.3461-0.08930.3445-22.263428.410245.4793
36.27990.1561-1.19183.30620.77656.95740.0342-0.0793-0.09850.41130.0615-0.91360.36080.9013-0.0970.16010.040.01420.3301-0.03310.6761-11.464117.504540.303
47.6646-0.0346-0.49426.6278-0.24556.56220.24460.0711-0.3872-0.37740.1285-1.01881.07870.9673-0.28720.46360.1391-0.00710.4362-0.13390.4878-13.55193.185228.2115
57.9859-0.78711.14716.50350.49078.61840.24180.7549-0.7654-0.6506-0.03010.68310.59030.5718-0.11470.49880.0764-0.07140.3729-0.08750.4281-27.23510.595916.2456
61.2323-2.3458-0.56764.85811.02343.2830.2860.5123-0.2265-0.9383-0.36860.7823-0.245-0.72490.23220.49490.0374-0.24060.3785-0.13220.4776-42.788211.399314.0848
77.26030.12331.1146.10621.73516.60420.14770.03170.3027-0.04310.16610.5736-0.4278-0.7103-0.2860.1899-0.0208-0.02420.31890.08960.3619-48.83128.312124.8638
83.08581.1925-0.57485.0756-2.01762.48340.0907-0.135-0.09080.4770.42281.0753-0.3363-0.6064-0.39530.45380.055-0.01070.37810.01790.3672-54.967421.436570.8971
92.07060.2775-0.63584.77570.14435.04680.43380.10540.0781-1.11640.17391.04860.383-0.80720.63880.69730.0498-0.33710.2575-0.12850.4097-55.04478.322855.0095
103.34140.8782-0.42614.2506-0.32072.33110.23260.249-0.6818-0.5189-0.06111.09620.7039-0.5221-0.01790.8487-0.2184-0.40370.2156-0.10670.8786-53.0368-6.819562.2218
115.551-1.36870.0235.56551.23428.2438-0.39490.1901-1.0367-0.61650.39660.49661.25820.2341-0.01120.8332-0.0181-0.11260.28350.02420.6166-37.4648-12.959271.3356
125.03940.82010.62525.613-1.32125.0564-0.1109-0.1409-0.7260.39330.0456-0.50430.89220.00550.09810.73920.1389-0.17810.2766-0.01720.3157-27.4979-4.164983.0247
134.438-2.0480.37865.42021.98685.0657-0.0483-0.01310.11791.10330.0263-0.7656-0.320.94510.02230.6749-0.0596-0.22740.37030.01370.4429-25.739513.294185.7057
143.14582.0684-0.20912.7950.55983.5950.0998-0.3550.26581.0466-0.0358-0.2753-1.28270.1325-0.08910.82910.0719-0.02390.3088-0.03660.3361-36.549630.048572.6282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L
13X-RAY DIFFRACTION13chain M
14X-RAY DIFFRACTION14chain N

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