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- PDB-4m77: Crystal structure of Lsm2-8 complex, space group I212121 -

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Basic information

Entry
Database: PDB / ID: 4m77
TitleCrystal structure of Lsm2-8 complex, space group I212121
Components(U6 snRNA-associated Sm-like protein ...) x 7
KeywordsSTRUCTURAL PROTEIN / Sm Like protein / RNA splicing
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
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: 3.111 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

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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)154,03614
Polymers154,03614
Non-polymers00
Water00
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)77,0187
Polymers77,0187
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-65 kcal/mol
Surface area22820 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)77,0187
Polymers77,0187
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-70 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.103, 145.878, 149.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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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: 12355.225 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 20% PEG2000MME, 100mM Sodium Citrate 5.2, 10% 2-propanol, 50mM 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: Jul 12, 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: 3.1→40 Å / Num. all: 27294 / Num. obs: 26475 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.1→3.21 Å / % possible all: 98.9

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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 4M75

4m75


Resolution: 3.111→29.979 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 1330 5.02 %random
Rwork0.2466 ---
obs0.2477 26470 96 %-
all-27573 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.987 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7954 Å20 Å20 Å2
2--1.9331 Å20 Å2
3---0.5063 Å2
Refinement stepCycle: LAST / Resolution: 3.111→29.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8312 0 0 0 8312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098397
X-RAY DIFFRACTIONf_angle_d1.31811329
X-RAY DIFFRACTIONf_dihedral_angle_d19.1923097
X-RAY DIFFRACTIONf_chiral_restr0.0821388
X-RAY DIFFRACTIONf_plane_restr0.0051416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1114-3.22250.39531270.35582255X-RAY DIFFRACTION88
3.2225-3.35140.36661510.32722536X-RAY DIFFRACTION99
3.3514-3.50370.31121390.28682571X-RAY DIFFRACTION99
3.5037-3.68810.27811200.27492576X-RAY DIFFRACTION99
3.6881-3.91870.32211380.2722569X-RAY DIFFRACTION99
3.9187-4.22050.27241480.24392532X-RAY DIFFRACTION98
4.2205-4.64380.21681260.18912568X-RAY DIFFRACTION97
4.6438-5.31260.22561260.20372511X-RAY DIFFRACTION96
5.3126-6.68110.30571150.27462529X-RAY DIFFRACTION94
6.6811-29.98010.22561400.23172493X-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)
13.91693.0398-1.45044.66791.00283.7413-0.03130.4303-0.0061-0.33980.04150.1842-0.33750.2555-0.08790.56940.20710.0430.5533-0.09370.53099.8807-13.6403-4.3637
25.4152-1.1651-3.1142.94770.08887.6446-0.288-0.343-0.4520.04880.0920.04890.28230.38020.17810.50590.0711-0.04490.4761-0.02150.51596.2636-21.566312.7446
36.7718-1.19930.02734.21161.21474.51690.2418-0.0285-0.5476-0.09610.23630.39890.3175-0.1913-0.43860.6184-0.0190.04240.6205-0.00920.7337-9.0011-22.007717.6127
47.43081.1536-0.15736.096-1.52066.74570.3026-0.6926-0.46560.2592-0.09150.37450.1262-0.8664-0.12910.54060.1039-0.02310.6966-0.02030.5746-22.8687-8.630416.7886
58.14522.24142.25546.2584-0.33075.05490.5519-0.5615-0.19280.0938-0.26260.0501-0.1046-0.041-0.19750.46650.07740.06170.4882-0.15640.5023-23.34056.56066.3477
67.2903-1.6728-0.21784.167-1.0944.95660.46940.37720.4679-0.2549-0.2577-0.743-0.4871-0.1768-0.16270.6240.15920.14650.5988-0.07850.7551-11.390212.4425-5.8555
75.4365-0.12142.95833.5072-1.31173.08630.21860.6160.8025-0.002-0.0057-0.0909-0.04890.1029-0.31690.72110.13360.21830.7673-0.02060.7367.5465.4885-8.6056
81.21670.5148-1.46282.97252.03482.8751-0.15890.3621-0.22160.0380.06590.0135-0.0626-0.12310.09240.5492-0.08660.03550.48450.24460.52241.2664-22.456325.4934
96.3083-0.388-2.88712.65740.14127.4102-0.23390.41840.4405-0.02630.2112-0.2946-0.56530.0178-0.05630.6174-0.0267-0.0350.42720.07960.615724.5693-14.955829.1225
104.58240.99020.63026.3326-1.97927.8194-0.1622-0.10860.29810.29270.0217-0.246-1.00890.06240.13280.61150.030.06220.34590.05690.448122.0285-14.05645.1127
116.2820.68083.25524.2234-0.66186.10440.1705-0.8129-0.00320.9089-0.18020.4384-0.2914-0.4444-0.02850.9281-0.0160.12410.68360.09690.592423.1985-27.587858.5589
125.22640.4819-0.12795.0360.37246.9163-0.3038-0.3778-0.07390.4039-0.1224-0.569-0.0728-0.09970.44920.532-0.1099-0.01470.53390.16410.429933.9168-42.115258.5784
133.6096-1.1324-1.05355.4028-2.08586.9657-0.2377-0.3528-0.3234-0.2693-0.4811-1.06670.6860.9740.71830.63810.01430.1770.62060.21060.907344.8917-48.65745.8453
143.9034-2.54782.13664.64031.31314.818-0.20330.0704-0.3375-0.0021-0.4386-0.82980.89120.72720.55660.6353-0.03930.34120.71550.16770.795646.3627-41.667626.7556
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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