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- PDB-4n0a: Crystal structure of Lsm2-3-Pat1C complex from Saccharomyces cere... -

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Basic information

Entry
Database: PDB / ID: 4n0a
TitleCrystal structure of Lsm2-3-Pat1C complex from Saccharomyces cerevisiae
Components
  • DNA topoisomerase 2-associated protein PAT1
  • U6 snRNA-associated Sm-like protein LSm2
  • U6 snRNA-associated Sm-like protein LSm3
KeywordsRNA BINDING PROTEIN / Decapping activator
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 / formation of translation preinitiation complex / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / P-body assembly / regulation of translational initiation / tRNA processing ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / P-body assembly / regulation of translational initiation / tRNA processing / precatalytic spliceosome / cellular response to glucose starvation / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / negative regulation of translational initiation / spliceosomal complex / P-body / mRNA splicing, via spliceosome / kinetochore / mRNA processing / cytoplasmic stress granule / rRNA processing / cytosolic small ribosomal subunit / cell division / mRNA binding / chromatin binding / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins ...mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / 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
Deadenylation-dependent mRNA-decapping factor PAT1 / LSM complex subunit LSM2 / LSM complex subunit LSM3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.15 Å
AuthorsWu, D.H.
CitationJournal: Cell Res. / Year: 2014
Title: Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation
Authors: Wu, D. / Muhlrad, D. / Bowler, M.W. / Jiang, S. / Liu, Z. / Parker, R. / Song, H.
History
DepositionOct 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 LSm3
B: U6 snRNA-associated Sm-like protein LSm3
C: U6 snRNA-associated Sm-like protein LSm2
D: U6 snRNA-associated Sm-like protein LSm2
E: U6 snRNA-associated Sm-like protein LSm3
F: U6 snRNA-associated Sm-like protein LSm3
G: U6 snRNA-associated Sm-like protein LSm2
H: DNA topoisomerase 2-associated protein PAT1
I: DNA topoisomerase 2-associated protein PAT1
J: DNA topoisomerase 2-associated protein PAT1


Theoretical massNumber of molelcules
Total (without water)208,11810
Polymers208,11810
Non-polymers00
Water1,38777
1
A: U6 snRNA-associated Sm-like protein LSm3
B: U6 snRNA-associated Sm-like protein LSm3
C: U6 snRNA-associated Sm-like protein LSm2
D: U6 snRNA-associated Sm-like protein LSm2
E: U6 snRNA-associated Sm-like protein LSm3
F: U6 snRNA-associated Sm-like protein LSm3
G: U6 snRNA-associated Sm-like protein LSm2

A: U6 snRNA-associated Sm-like protein LSm3
B: U6 snRNA-associated Sm-like protein LSm3
C: U6 snRNA-associated Sm-like protein LSm2
D: U6 snRNA-associated Sm-like protein LSm2
E: U6 snRNA-associated Sm-like protein LSm3
F: U6 snRNA-associated Sm-like protein LSm3
G: U6 snRNA-associated Sm-like protein LSm2


Theoretical massNumber of molelcules
Total (without water)157,09414
Polymers157,09414
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area30260 Å2
ΔGint-141 kcal/mol
Surface area51240 Å2
MethodPISA
2
H: DNA topoisomerase 2-associated protein PAT1


Theoretical massNumber of molelcules
Total (without water)43,1901
Polymers43,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
I: DNA topoisomerase 2-associated protein PAT1


Theoretical massNumber of molelcules
Total (without water)43,1901
Polymers43,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
J: DNA topoisomerase 2-associated protein PAT1


Theoretical massNumber of molelcules
Total (without water)43,1901
Polymers43,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.447, 251.511, 120.310
Angle α, β, γ (deg.)90.00, 112.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
U6 snRNA-associated Sm-like protein LSm3 / SmX4 protein


Mass: 10039.262 Da / Num. of mol.: 4
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
#2: Protein U6 snRNA-associated Sm-like protein LSm2 / Small nuclear ribonucleoprotein D homolog SNP3


Mass: 12796.582 Da / Num. of mol.: 3
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 DNA topoisomerase 2-associated protein PAT1 / Decapping activator and translational repressor PAT1 / Topoisomerase II-associated protein PAT1 / ...Decapping activator and translational repressor PAT1 / Topoisomerase II-associated protein PAT1 / mRNA turnover protein 1


Mass: 43190.473 Da / Num. of mol.: 3 / Fragment: UNP residues 423-796 / Mutation: D688V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MRT1, PAT1, YCR077C, YCR77C / Production host: Escherichia coli (E. coli) / References: UniProt: P25644
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 4.66 Å3/Da / Density % sol: 73.62 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris, 12% ethanol, pH 7.0, 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: 1.072, 1.2553, 1.2557, 1.2427
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0721
21.25531
31.25571
41.24271
ReflectionResolution: 3.15→19.9 Å / Num. all: 65278 / Num. obs: 65011 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.15→3.2621 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 3.15→19.884 Å / SU ML: 0.45 / σ(F): 1 / Phase error: 38.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3002 3250 5.07 %RANDOM
Rwork0.2722 ---
obs0.2736 65011 98.61 %-
all-65278 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.001 Å2 / ksol: 0.272 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-101.3454 Å20 Å218.7384 Å2
2--30.8795 Å2-0 Å2
3---27.3943 Å2
Refinement stepCycle: LAST / Resolution: 3.15→19.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12268 0 0 77 12345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712427
X-RAY DIFFRACTIONf_angle_d1.11316754
X-RAY DIFFRACTIONf_dihedral_angle_d18.0944729
X-RAY DIFFRACTIONf_chiral_restr0.0752008
X-RAY DIFFRACTIONf_plane_restr0.0032102
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 (%)
3.15-3.26210.44966020.45171223199
3.2621-3.39210.45887080.4111215299
3.3921-3.54570.3786590.36931210898
3.5457-3.73140.36516530.35741186397
3.7314-3.96350.36566430.32531187996
3.9635-4.26670.34286100.29651225299
4.2667-4.6910.2846120.25741221499
4.691-5.35820.30196730.26311223599
5.3582-6.70740.34176140.288412331100
6.7074-19.88440.20636990.18421202098

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