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- PDB-4m78: Crystal structure of Lsm2-8 complex, space group P21 -

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Basic information

Entry
Database: PDB / ID: 4m78
TitleCrystal structure of Lsm2-8 complex, space group P21
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 / 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 / U2-type prespliceosome ...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 / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / 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 / rRNA processing / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
Sm-like protein Lsm8 / 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 Lsm8 / 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 / U6 snRNA-associated Sm-like protein LSm8 / 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: 2.794 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 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 LSm8
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 LSm8
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)150,77014
Polymers150,77014
Non-polymers00
Water95553
1
A: U6 snRNA-associated Sm-like protein LSm8
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


Theoretical massNumber of molelcules
Total (without water)75,3857
Polymers75,3857
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12030 Å2
ΔGint-62 kcal/mol
Surface area22430 Å2
MethodPISA
2
H: U6 snRNA-associated Sm-like protein LSm8
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)75,3857
Polymers75,3857
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-58 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.721, 76.638, 113.554
Angle α, β, γ (deg.)90.00, 97.00, 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 ... , 7 types, 14 molecules AHBICJDKELFMGN

#1: Protein U6 snRNA-associated Sm-like protein LSm8


Mass: 10722.324 Da / Num. of mol.: 2 / Mutation: K17L,C22S,I38L,C51S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM8, YJR022W, J1464, YJR83.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P47093
#2: Protein U6 snRNA-associated Sm-like protein LSm2 / Small nuclear ribonucleoprotein D homolog SNP3


Mass: 11161.822 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 / SmX4 protein


Mass: 10007.131 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: 9406.579 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: LSM6, YDR378C, D9481.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06406
#5: Protein U6 snRNA-associated Sm-like protein LSm5


Mass: 10432.954 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: 13027.045 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: LSM7, YNL147W, N1202, N1780 / Production host: Escherichia coli (E. coli) / References: UniProt: P53905
#7: Protein U6 snRNA-associated Sm-like protein LSm4


Mass: 10627.117 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: LSM4, SDB23, USS1, YER112W / Production host: Escherichia coli (E. coli) / References: UniProt: P40070

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Non-polymers , 1 types, 53 molecules

#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM sodium cacodylate 6.5, 25% Jeffamine ED2001, 20mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Apr 8, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.794→30 Å / Num. all: 34154 / Num. obs: 33539 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.794→2.9 Å / % possible all: 83

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Processing

Software
NameVersionClassification
ADSCQuantumdata 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 4M75

4m75


Resolution: 2.794→29.068 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 30.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2936 1702 5.08 %
Rwork0.2535 --
obs0.2555 33508 98.67 %
all-33960 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.477 Å2 / ksol: 0.296 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1482 Å20 Å20.0606 Å2
2--9.462 Å20 Å2
3---2.6133 Å2
Refinement stepCycle: LAST / Resolution: 2.794→29.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8112 0 0 53 8165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118192
X-RAY DIFFRACTIONf_angle_d1.37611045
X-RAY DIFFRACTIONf_dihedral_angle_d18.713043
X-RAY DIFFRACTIONf_chiral_restr0.0921358
X-RAY DIFFRACTIONf_plane_restr0.0041378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7938-2.87590.42971100.40412299X-RAY DIFFRACTION86
2.8759-2.96870.44121640.38152638X-RAY DIFFRACTION99
2.9687-3.07470.38561550.33622668X-RAY DIFFRACTION100
3.0747-3.19760.3291400.31272656X-RAY DIFFRACTION100
3.1976-3.34290.34351540.27842668X-RAY DIFFRACTION100
3.3429-3.51890.31831240.25522669X-RAY DIFFRACTION100
3.5189-3.7390.29111350.24262674X-RAY DIFFRACTION100
3.739-4.0270.29131330.24762701X-RAY DIFFRACTION100
4.027-4.43090.25851400.21162698X-RAY DIFFRACTION100
4.4309-5.06920.21121570.18392671X-RAY DIFFRACTION100
5.0692-6.37550.3021370.26672705X-RAY DIFFRACTION100
6.3755-29.06990.29181530.25822759X-RAY DIFFRACTION100
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)
17.4453-0.24480.71362.0328-0.24897.8425-0.08540.7290.6241-0.27940.0205-0.02610.11480.15280.17930.3018-0.0283-0.01270.34510.07770.385977.93515.956328.8191
26.21-0.0652.53575.2808-0.55665.5774-0.66830.16210.8518-0.18440.5081-0.0593-0.4810.09550.10630.2659-0.0353-0.0430.4138-0.04730.516794.269318.046542.1018
33.7296-0.3852-0.06363.5449-0.63983.8447-0.193-0.18920.12790.06190.1542-0.45990.0276-0.0741-0.02470.15150.0840.02430.4476-0.07870.3495102.14883.706846.4393
43.93931.2813-1.17144.89930.63984.43140.241-0.8563-0.03410.6740.23760.0139-0.1719-0.0677-0.2540.40890.08310.09510.56060.08020.263494.9512-11.03256.2418
54.4979-0.06320.35081.8819-0.47122.98240.0216-0.9113-1.15450.66840.16110.27520.43990.10160.09720.2150.20640.13980.02590.24850.515478.9384-18.348452.9953
64.67150.84052.6335.7448-2.094.5734-0.1772-0.1557-0.4855-0.23230.43370.57270.4363-0.2605-0.26570.2846-0.01960.05150.3390.03760.409965.2282-13.156942.5182
76.1591.866-0.46476.19430.77714.9518-0.15260.60950.3856-0.42070.30240.6725-0.1053-0.3394-0.1470.3024-0.0082-0.05460.39680.02780.36964.26194.218532.0781
84.48131.00741.58444.649-1.10227.0720.2889-0.32390.0302-0.0577-0.07510.97980.7026-0.9384-0.150.3895-0.1559-0.03470.4630.02590.531693.924-35.631810.0794
96.5193-0.51252.39196.68831.38954.63320.2414-0.444-0.69310.29710.18480.29230.9958-0.3181-0.25020.4668-0.0153-0.08890.33390.03390.3382110.3783-37.164323.6215
104.0103-0.2446-1.26596.28691.60754.68650.0695-0.0867-0.02150.41170.154-0.01990.2659-0.0075-0.19830.266-0.0213-0.01070.3741-0.02480.2433115.2208-22.510930.4581
116.3063-0.1872-0.7565.5766-0.95175.7828-0.32810.08350.14710.1170.2687-0.6016-0.0780.33220.08150.2051-0.07330.01960.3339-0.05440.3024122.5589-7.654621.3744
124.10250.70780.85662.87690.40817.2848-0.0917-0.16840.4499-0.5372-0.1023-0.4353-0.8990.48420.06880.4272-0.0690.02460.1311-0.04320.1912116.2465-0.755.6219
136.78482.30540.74526.76350.47054.212-0.0333-0.07850.5099-0.3871-0.0780.5761-0.3712-0.36430.06240.47690.0541-0.08150.3314-0.01680.3103103.6789-6.2914-5.4894
144.9746-1.0467-0.40755.9426-0.31145.32360.08590.4285-0.0161-0.6988-0.01510.34460.3184-0.44090.06040.3668-0.0434-0.15550.3803-0.01040.345194.053-24.2571-4.2949
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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