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- PDB-4emh: Crystal structure of SpLsm4 -

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Basic information

Entry
Database: PDB / ID: 4emh
TitleCrystal structure of SpLsm4
ComponentsProbable U6 snRNA-associated Sm-like protein LSm4
KeywordsRNA BINDING PROTEIN / Sm fold / mRNA decay / pre-mRNA splicing / Lsm proteins
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / Lsm1-7-Pat1 complex / U6 snRNP / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P-body assembly / U2 snRNP / telomerase holoenzyme complex assembly / nuclear-transcribed mRNA catabolic process ...mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / Lsm1-7-Pat1 complex / U6 snRNP / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P-body assembly / U2 snRNP / telomerase holoenzyme complex assembly / nuclear-transcribed mRNA catabolic process / U5 snRNP / RNA folding / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / P-body / nucleolus / nucleus / cytosol
Similarity search - Function
Sm-like protein Lsm4 / SH3 type barrels. - #100 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...Sm-like protein Lsm4 / SH3 type barrels. - #100 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / 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
LSM complex subunit lsm4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJiang, S.M. / Wu, D.H. / Song, H.W.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structures of Lsm3, Lsm4 and Lsm5/6/7 from Schizosaccharomyces pombe.
Authors: Wu, D.H. / Jiang, S.M. / Bowler, M.W. / Song, H.W.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable U6 snRNA-associated Sm-like protein LSm4
B: Probable U6 snRNA-associated Sm-like protein LSm4
C: Probable U6 snRNA-associated Sm-like protein LSm4
D: Probable U6 snRNA-associated Sm-like protein LSm4
E: Probable U6 snRNA-associated Sm-like protein LSm4
F: Probable U6 snRNA-associated Sm-like protein LSm4
G: Probable U6 snRNA-associated Sm-like protein LSm4
H: Probable U6 snRNA-associated Sm-like protein LSm4
I: Probable U6 snRNA-associated Sm-like protein LSm4
J: Probable U6 snRNA-associated Sm-like protein LSm4
K: Probable U6 snRNA-associated Sm-like protein LSm4
L: Probable U6 snRNA-associated Sm-like protein LSm4
M: Probable U6 snRNA-associated Sm-like protein LSm4
N: Probable U6 snRNA-associated Sm-like protein LSm4
O: Probable U6 snRNA-associated Sm-like protein LSm4
P: Probable U6 snRNA-associated Sm-like protein LSm4
Q: Probable U6 snRNA-associated Sm-like protein LSm4
R: Probable U6 snRNA-associated Sm-like protein LSm4
T: Probable U6 snRNA-associated Sm-like protein LSm4
U: Probable U6 snRNA-associated Sm-like protein LSm4
V: Probable U6 snRNA-associated Sm-like protein LSm4
W: Probable U6 snRNA-associated Sm-like protein LSm4
X: Probable U6 snRNA-associated Sm-like protein LSm4
Y: Probable U6 snRNA-associated Sm-like protein LSm4


Theoretical massNumber of molelcules
Total (without water)297,89824
Polymers297,89824
Non-polymers00
Water19,1501063
1
A: Probable U6 snRNA-associated Sm-like protein LSm4
B: Probable U6 snRNA-associated Sm-like protein LSm4
C: Probable U6 snRNA-associated Sm-like protein LSm4


Theoretical massNumber of molelcules
Total (without water)37,2373
Polymers37,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Probable U6 snRNA-associated Sm-like protein LSm4
E: Probable U6 snRNA-associated Sm-like protein LSm4
F: Probable U6 snRNA-associated Sm-like protein LSm4


Theoretical massNumber of molelcules
Total (without water)37,2373
Polymers37,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Probable U6 snRNA-associated Sm-like protein LSm4
H: Probable U6 snRNA-associated Sm-like protein LSm4
I: Probable U6 snRNA-associated Sm-like protein LSm4


Theoretical massNumber of molelcules
Total (without water)37,2373
Polymers37,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Probable U6 snRNA-associated Sm-like protein LSm4
K: Probable U6 snRNA-associated Sm-like protein LSm4
L: Probable U6 snRNA-associated Sm-like protein LSm4


Theoretical massNumber of molelcules
Total (without water)37,2373
Polymers37,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Probable U6 snRNA-associated Sm-like protein LSm4
N: Probable U6 snRNA-associated Sm-like protein LSm4
O: Probable U6 snRNA-associated Sm-like protein LSm4


Theoretical massNumber of molelcules
Total (without water)37,2373
Polymers37,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: Probable U6 snRNA-associated Sm-like protein LSm4
Q: Probable U6 snRNA-associated Sm-like protein LSm4
R: Probable U6 snRNA-associated Sm-like protein LSm4


Theoretical massNumber of molelcules
Total (without water)37,2373
Polymers37,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
T: Probable U6 snRNA-associated Sm-like protein LSm4
U: Probable U6 snRNA-associated Sm-like protein LSm4
V: Probable U6 snRNA-associated Sm-like protein LSm4


Theoretical massNumber of molelcules
Total (without water)37,2373
Polymers37,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
W: Probable U6 snRNA-associated Sm-like protein LSm4
X: Probable U6 snRNA-associated Sm-like protein LSm4
Y: Probable U6 snRNA-associated Sm-like protein LSm4


Theoretical massNumber of molelcules
Total (without water)37,2373
Polymers37,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.121, 124.470, 131.567
Angle α, β, γ (deg.)90.00, 135.07, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 13:71 )
211CHAIN B AND (RESSEQ 13:71 )
311CHAIN C AND (RESSEQ 13:71 )
411CHAIN D AND (RESSEQ 13:71 )
511CHAIN E AND (RESSEQ 13:71 )
611CHAIN F AND (RESSEQ 13:71 )
711CHAIN G AND (RESSEQ 13:71 )
811CHAIN H AND (RESSEQ 13:71 )
911CHAIN I AND (RESSEQ 13:71 )
1011CHAIN J AND (RESSEQ 13:71 )
1111CHAIN K AND (RESSEQ 13:71 )
1211CHAIN L AND (RESSEQ 13:71 )
1311CHAIN M AND (RESSEQ 13:71 )
1411CHAIN N AND (RESSEQ 13:71 )
1511CHAIN O AND (RESSEQ 13:71 )
1611CHAIN P AND (RESSEQ 13:71 )
1711CHAIN Q AND (RESSEQ 13:71 )
1811CHAIN R AND (RESSEQ 13:71 )
1911CHAIN T AND (RESSEQ 13:71 )
2011CHAIN U AND (RESSEQ 13:71 )
2111CHAIN V AND (RESSEQ 13:71 )
2211CHAIN W AND (RESSEQ 13:71 )
2311CHAIN X AND (RESSEQ 13:71 )
2411CHAIN Y AND (RESSEQ 13:71 )

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Components

#1: Protein ...
Probable U6 snRNA-associated Sm-like protein LSm4


Mass: 12412.400 Da / Num. of mol.: 24 / Fragment: UNP RESIDUES 1-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: lsm4, SPBC30D10.06 / Production host: Escherichia coli (E. coli) / References: UniProt: O14352
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1063 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, pH6.5, 0.1M NaCl, 12% polyethylene glycol (PEG) 4000, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2009
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: 2.2→92.91 Å / Num. all: 105873 / Num. obs: 105873 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.24 Å / % possible all: 91.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→92.559 Å / SU ML: 0.31 / σ(F): 1 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 2034 1.93 %Random
Rwork0.2373 ---
all0.2376 105147 --
obs0.2376 105147 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.536 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4326 Å20 Å20.8498 Å2
2--1.721 Å20 Å2
3---1.7117 Å2
Refinement stepCycle: LAST / Resolution: 2.2→92.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11928 0 0 1063 12991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112143
X-RAY DIFFRACTIONf_angle_d1.30816319
X-RAY DIFFRACTIONf_dihedral_angle_d13.9024775
X-RAY DIFFRACTIONf_chiral_restr0.1161728
X-RAY DIFFRACTIONf_plane_restr0.0052160
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A493X-RAY DIFFRACTIONPOSITIONAL
12B493X-RAY DIFFRACTIONPOSITIONAL0.092
13C493X-RAY DIFFRACTIONPOSITIONAL0.068
14D493X-RAY DIFFRACTIONPOSITIONAL0.074
15E493X-RAY DIFFRACTIONPOSITIONAL0.073
16F493X-RAY DIFFRACTIONPOSITIONAL0.082
17G493X-RAY DIFFRACTIONPOSITIONAL0.084
18H493X-RAY DIFFRACTIONPOSITIONAL0.103
19I493X-RAY DIFFRACTIONPOSITIONAL0.075
110J493X-RAY DIFFRACTIONPOSITIONAL0.082
111K493X-RAY DIFFRACTIONPOSITIONAL0.085
112L493X-RAY DIFFRACTIONPOSITIONAL0.093
113M493X-RAY DIFFRACTIONPOSITIONAL0.077
114N493X-RAY DIFFRACTIONPOSITIONAL0.088
115O493X-RAY DIFFRACTIONPOSITIONAL0.078
116P493X-RAY DIFFRACTIONPOSITIONAL0.098
117Q493X-RAY DIFFRACTIONPOSITIONAL0.085
118R493X-RAY DIFFRACTIONPOSITIONAL0.067
119T493X-RAY DIFFRACTIONPOSITIONAL0.085
120U493X-RAY DIFFRACTIONPOSITIONAL0.077
121V492X-RAY DIFFRACTIONPOSITIONAL0.054
122W493X-RAY DIFFRACTIONPOSITIONAL0.085
123X493X-RAY DIFFRACTIONPOSITIONAL0.072
124Y493X-RAY DIFFRACTIONPOSITIONAL0.106
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.27870.34292010.2798958492
2.2787-2.36990.30491990.25721028298
2.3699-2.47780.29572090.25211028399
2.4778-2.60840.26651950.25291033099
2.6084-2.77180.27771970.24081037699
2.7718-2.98590.26062060.245610373100
2.9859-3.28640.23612040.235410485100
3.2864-3.76190.24522070.221310423100
3.7619-4.73960.24552060.203710455100
4.7396-92.64060.19532100.24141052299

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