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- PDB-4m7d: Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU -

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Basic information

Entry
Database: PDB / ID: 4m7d
TitleCrystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU
Components
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • U6 snRNA
KeywordsRNA BINDING PROTEIN / Sm Like Fold / RNA splicing / STRUCTURAL PROTEIN-RNA complex
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 / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / P-body assembly / U2-type prespliceosome / tRNA processing ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / P-body assembly / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / nuclear-transcribed mRNA catabolic process / U6 snRNA binding / spliceosomal snRNP assembly / cellular response to glucose starvation / 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 / mRNA binding / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Sm-like protein Lsm7 / U6 snRNA-associated Sm-like protein Lsm1/8 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG ...Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Sm-like protein Lsm7 / U6 snRNA-associated Sm-like protein Lsm1/8 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / 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
RNA / LSM complex subunit LSM2 / LSM complex subunit LSM4 / LSM complex subunit LSM5 / LSM2-LSM8 complex subunit LSM8 / LSM complex subunit LSM7 / LSM complex subunit LSM3 / LSM complex subunit LSM6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.595 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
O: U6 snRNA
P: U6 snRNA


Theoretical massNumber of molelcules
Total (without water)155,65516
Polymers155,65516
Non-polymers00
Water1,62190
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
P: U6 snRNA


Theoretical massNumber of molelcules
Total (without water)77,8278
Polymers77,8278
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-71 kcal/mol
Surface area22890 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
O: U6 snRNA


Theoretical massNumber of molelcules
Total (without water)77,8278
Polymers77,8278
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-73 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.539, 78.483, 142.987
Angle α, β, γ (deg.)90.00, 103.17, 90.00
Int Tables number5
Space group name H-MC121

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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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RNA chain / Non-polymers , 2 types, 92 molecules OP

#8: RNA chain U6 snRNA


Mass: 2442.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligo is synthesized by TAKARA
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Sodium cacodylate 6.5, 25% Jeffamine ED2001, 5mM MgCl2, 8mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.595→40 Å / Num. all: 41994 / Num. obs: 41448 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.595→2.69 Å / % possible all: 95

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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 4M7A

4m7a


Resolution: 2.595→34.184 Å / SU ML: 0.47 / σ(F): 1.34 / Phase error: 31.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 2098 5.06 %random
Rwork0.2399 ---
obs0.242 41437 98.35 %-
all-42559 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.081 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.304 Å2-0 Å2-4.7817 Å2
2---2.4816 Å2-0 Å2
3----1.6292 Å2
Refinement stepCycle: LAST / Resolution: 2.595→34.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8179 186 0 90 8455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118458
X-RAY DIFFRACTIONf_angle_d1.46511438
X-RAY DIFFRACTIONf_dihedral_angle_d20.3413171
X-RAY DIFFRACTIONf_chiral_restr0.0881407
X-RAY DIFFRACTIONf_plane_restr0.0091400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5948-2.65520.39681310.37972328X-RAY DIFFRACTION88
2.6552-2.72150.46681350.37522659X-RAY DIFFRACTION99
2.7215-2.79510.3471530.35222594X-RAY DIFFRACTION99
2.7951-2.87730.4221560.33132595X-RAY DIFFRACTION99
2.8773-2.97010.35851320.31812668X-RAY DIFFRACTION99
2.9701-3.07620.39821380.30342648X-RAY DIFFRACTION99
3.0762-3.19930.31241570.29782590X-RAY DIFFRACTION99
3.1993-3.34480.32561150.26562655X-RAY DIFFRACTION99
3.3448-3.52090.29441440.24772665X-RAY DIFFRACTION99
3.5209-3.74130.29731450.24082621X-RAY DIFFRACTION99
3.7413-4.02970.28121700.23122628X-RAY DIFFRACTION99
4.0297-4.43450.25241180.19912665X-RAY DIFFRACTION99
4.4345-5.07440.18331300.16312675X-RAY DIFFRACTION99
5.0744-6.38640.27421390.24152689X-RAY DIFFRACTION99
6.3864-34.18740.25461350.23142659X-RAY DIFFRACTION96
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)
17.6038-1.26662.31728.0589-0.32974.31850.3377-0.3618-0.32820.8131-0.09720.43130.3572-0.7035-0.16220.5777-0.06870.08640.5580.08270.5615-19.0064-3.5281160.428
27.3411-0.89140.47216.98631.04932.6850.0817-0.5265-0.74350.5660.22520.0090.58060.2357-0.34330.740.121-0.12480.4515-0.0190.40742.145-5.194164.6668
32.5234-0.2911-2.06154.86682.78128.7805-0.1381-0.2641-0.10460.79240.4631-0.51840.55740.3416-0.37510.53080.0457-0.10490.4645-0.03460.398310.40718.761167.479
47.164-2.39620.19548.0142-1.03798.225-0.11130.25530.1399-0.14940.3126-0.71710.20030.4496-0.16920.4927-0.13820.01290.6124-0.03330.440712.983523.8266156.4068
56.94922.20073.12054.3917-0.10874.5526-0.30240.32950.4726-0.50740.26080.0813-0.6270.59050.11710.5311-0.08420.01530.25570.03850.2552-0.615631.4988146.3289
65.72854.2011-2.69747.6876-0.78116.2349-0.1040.12110.7958-0.48480.05280.7228-0.5337-0.33730.0310.5393-0.0091-0.13860.39050.0550.4993-17.011825.9576142.8781
77.5861-1.83932.98623.43790.02637.2305-0.1923-0.08710.05640.3976-0.14220.3317-0.1689-0.43640.31780.3814-0.00010.04970.50540.01920.5676-25.50278.6503148.8835
85.99911.4475-1.67616.1738-2.71513.48430.5171.12330.3526-1.6069-0.33121.0811-0.3805-1.2084-0.1420.87590.3397-0.21340.74150.1910.7624-23.244846.856182.5027
97.3738-1.01351.20127.89190.76245.02470.16860.43311.0405-0.90090.1177-0.4493-0.78950.147-0.17440.6858-0.00380.10320.41950.05920.6592-2.574948.5498188.2462
103.3511-0.78120.03716.96362.06315.83850.0950.32720.1853-0.610.2663-1.0001-0.15680.2867-0.33970.34570.02980.0690.2466-0.0110.27755.799134.2021188.8927
117.52011.9358-0.83344.5210.17125.11590.0425-0.4446-0.09380.50980.3081-0.29380.13440.6254-0.36830.66130.1259-0.0580.4791-0.01910.36562.707519.1849199.5564
126.20880.2286-3.81433.55190.36335.3907-0.2606-0.3688-0.72090.83480.27160.59980.45050.15150.150.69810.08510.15620.29950.08510.5316-13.948911.7927202.8543
134.7317-3.84131.38716.9975-0.03566.3112-0.06530.2363-0.15750.2310.02061.47980.2509-0.30490.13470.5819-0.09470.11190.52320.1041.1484-30.300917.3559198.5579
144.79254.2636-0.2274.57681.61427.50070.11260.5664-0.3047-0.0630.17541.9134-0.3576-1.2251-0.38150.68710.1545-0.16470.94370.06191.4243-34.242534.3813190.4266
159.5188-3.82694.6289.2899-1.32869.1589-0.629-0.3963-2.280.25460.89113.56690.7831-0.4548-0.30661.43980.0918-0.02130.8496-0.02051.8909-17.212135.8909199.1215
163.99023.47224.0793.81164.34334.9396-1.7753.62760.538-2.22940.51471.6722-1.97480.42951.24611.4119-0.2419-0.34721.4941-0.24941.3461-5.3286.2177150.0627
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
15X-RAY DIFFRACTION15chain O
16X-RAY DIFFRACTION16chain P

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