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- PDB-4m7a: Crystal structure of Lsm2-8 complex bound to the 3' end sequence ... -

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Basic information

Entry
Database: PDB / ID: 4m7a
TitleCrystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA
Components
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • U6 snRNAU6 spliceosomal RNA
KeywordsRNA BINDING PROTEIN / Sm Like protein / 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 / 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
RNA / 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: 2.781 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
Water0
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-72 kcal/mol
Surface area21890 Å2
MethodPISA
2
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-78 kcal/mol
Surface area22470 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29560 Å2
ΔGint-161 kcal/mol
Surface area42370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.624, 78.379, 140.565
Angle α, β, γ (deg.)90.00, 100.58, 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 , 1 types, 2 molecules OP

#8: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 2442.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The RNA oligo is synthesized by TAKARA

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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: 2.05 Å3/Da / Density % sol: 39.88 %
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: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.781→40 Å / Num. all: 31677 / Num. obs: 31170 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.781→2.9 Å / % possible all: 99.6

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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 4M78

4m78


Resolution: 2.781→39.189 Å / SU ML: 0.5 / σ(F): 1.34 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 1576 5.06 %random
Rwork0.2447 ---
obs0.2465 31163 97.9 %-
all-31831 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.987 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.536 Å2-0 Å2-10.0121 Å2
2---3.4226 Å20 Å2
3---11.1968 Å2
Refinement stepCycle: LAST / Resolution: 2.781→39.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8089 206 0 0 8295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098403
X-RAY DIFFRACTIONf_angle_d1.26911370
X-RAY DIFFRACTIONf_dihedral_angle_d20.5173152
X-RAY DIFFRACTIONf_chiral_restr0.0851403
X-RAY DIFFRACTIONf_plane_restr0.0041388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.781-2.87070.40291200.36292573X-RAY DIFFRACTION94
2.8707-2.97330.39461470.33272725X-RAY DIFFRACTION100
2.9733-3.09230.36911430.3182709X-RAY DIFFRACTION100
3.0923-3.2330.32931310.28862719X-RAY DIFFRACTION99
3.233-3.40330.31461380.25912735X-RAY DIFFRACTION99
3.4033-3.61640.2821470.25232686X-RAY DIFFRACTION99
3.6164-3.89540.30141400.25382723X-RAY DIFFRACTION98
3.8954-4.2870.28191600.22992659X-RAY DIFFRACTION98
4.287-4.90630.20991450.17422691X-RAY DIFFRACTION97
4.9063-6.17750.25871720.24332664X-RAY DIFFRACTION98
6.1775-39.19340.26621330.24882703X-RAY DIFFRACTION95
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)
19.0073-0.09941.15914.82140.56657.20290.8003-0.6194-0.16561.2744-0.4721-0.8131-0.06840.5687-0.29610.756-0.2498-0.09230.5534-0.02540.656410.79935.8911164.8863
27.5355-0.49533.76956.2971.01424.8942-0.1342-0.12711.09090.3877-0.00350.3169-0.5408-0.51610.13620.6257-0.00950.25280.36660.04030.676-10.31377.7565160.3242
30.98180.1151-1.57056.1046-3.98178.03250.0679-0.00280.27610.3290.27720.6481-0.3405-0.2234-0.32770.4651-0.04860.11450.54830.00440.5148-18.7781-6.5183158.8656
47.297-0.57350.66977.45211.52797.93570.30790.53590.004-0.33020.12020.49980.2186-0.7149-0.35470.3805-0.1756-0.04840.53440.02110.3723-16.2009-21.4948147.6796
56.4308-0.8426-2.98544.0396-0.43626.6557-0.05160.6398-0.2859-0.4380.2551-0.18460.3105-0.3926-0.18010.5456-0.05720.05310.3069-0.0880.40860.0722-29.1102144.1737
67.43052.28841.15058.2414-0.63835.97420.2804-0.4029-0.6048-0.25330.211-1.34840.09120.4693-0.55440.48670.04470.00160.5236-0.2530.801116.6563-23.7447148.1427
75.22570.71691.2634.0673-0.74392.5425-0.09070.11670.02480.65350.0026-1.2741-0.38050.77770.04060.5412-0.1874-0.22090.6666-0.07810.852421.7644-5.5506156.3202
82.9521-1.28960.48163.350.56172.50960.6658-0.45640.24590.02540.1868-1.61730.81281.0461-0.44650.57530.3444-0.25790.6171-0.53261.70066.4809-44.9903185.3829
93.33471.08290.86018.5078-0.51694.06220.45570.1004-0.8621-0.64730.2943-0.25971.0328-0.2824-0.69110.8245-0.0934-0.39480.43940.01390.7321-15.0387-46.5443182.3361
103.01351.6368-0.67695.1507-3.61294.80410.0330.085-0.4833-1.01040.40930.40940.6484-0.5847-0.40210.4534-0.0849-0.18550.44080.09180.421-23.0499-32.1454179.9429
114.56731.3159-0.1638.36380.29584.4728-0.0008-0.30010.07590.59130.50760.7025-0.1566-0.4361-0.60140.53530.14730.03570.60050.05780.4988-24.5779-17.3947191.1788
124.27940.67112.05194.35651.26018.1892-0.1658-0.4580.24610.67820.4055-0.3378-0.6213-0.4823-0.22750.67680.2093-0.18040.3823-0.1510.4638-10.9416-9.852200.4215
131.18740.34911.80012.84050.79642.9356-0.37710.3377-0.05150.56830.1723-1.8611-0.22311.3129-0.42560.6921-0.2628-0.69640.0709-0.39741.62886.0487-15.4288203.217
140.58841.31160.25833.3349-0.76932.836-0.0630.3064-0.73920.66960.2384-1.99350.0761.16960.00120.60130.0518-0.31920.6005-0.2831.914113.1345-33.0209197.5979
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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