4M75

Crystal structure of Lsm1-7 complex

> Summary

Summary for 4M75

Related4M77 4M78 4M7A 4M7D
DescriptorLsm1, Lsm2, Lsm3, Lsm4, Lsm5, Lsm6, Lsm7
Functional Keywordssm like protein, rna splicing, structural protein, rna binding protein
Biological sourceSaccharomyces cerevisiae (Baker's yeast)
Cellular locationNucleus P47017 P38203 P57743 P40089 P53905 P40070
Cytoplasm Q06406
Total number of polymer chains14
Total molecular weight172768.62
Authors
Zhou, L.,Hang, J.,Zhou, Y.,Wan, R.,Lu, G.,Yan, C.,Shi, Y. (deposition date: 2013-08-12, release date: 2013-10-23, modification date: 2014-02-19)
Primary citation
Zhou, L.,Hang, J.,Zhou, Y.,Wan, R.,Lu, G.,Yin, P.,Yan, C.,Shi, Y.
Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA.
Nature, 506:116-120, 2014
PubMed: 24240276
DOI: 10.1038/nature12803
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.95 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.288620.9%22.7%5.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4m75
no rotation
Molmil generated image of 4m75
rotated about x axis by 90°
Molmil generated image of 4m75
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 4m75
no rotation
Molmil generated image of 4m75
rotated about x axis by 90°
Molmil generated image of 4m75
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (4m75.pdb1.gz [207.2 KB])
Coordinate files for Biological unit (4m75.pdb2.gz [200.25 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, HU6 snRNA-associated Sm-like protein Lsm1polymer14417474.02
UniProt (P47017)
Pfam (PF01423)
Saccharomyces cerevisiae (Baker's yeast)
B, IU6 snRNA-associated Sm-like protein Lsm2polymer9511302.62
UniProt (P38203)
Pfam (PF01423)
Saccharomyces cerevisiae (Baker's yeast)
C, JU6 snRNA-associated Sm-like protein Lsm3polymer8910101.02
UniProt (P57743)
Pfam (PF01423)
Saccharomyces cerevisiae (Baker's yeast)
D, KU6 snRNA-associated Sm-like protein Lsm6polymer869547.42
UniProt (Q06406)
Pfam (PF01423)
Saccharomyces cerevisiae (Baker's yeast)
E, LU6 snRNA-associated Sm-like protein Lsm5polymer9310573.72
UniProt (P40089)
Pfam (PF01423)
Saccharomyces cerevisiae (Baker's yeast)
F, MU6 snRNA-associated Sm-like protein Lsm7polymer11513261.62
UniProt (P53905)
Pfam (PF01423)
Saccharomyces cerevisiae (Baker's yeast)
G, NU6 snRNA-associated Sm-like protein Lsm4polymer12214088.52
UniProt (P40070)
Pfam (PF01423)
Saccharomyces cerevisiae (Baker's yeast)
CHLORIDE IONnon-polymer35.52

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains14
Total molecular weight172697.7
Non-Polymers*Number of molecules2
Total molecular weight70.9
All*Total molecular weight172768.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.95 Å)

Cell axes66.67267.83598.235
Cell angles93.14108.21116.30
SpacegroupP 1
Resolution limits38.66 - 2.95
the highest resolution shell value2.998 - 2.950
R-factor0.267
R-work0.26600
the highest resolution shell value0.401
R-free0.29100
the highest resolution shell value0.454
RMSD bond length0.019
RMSD bond angle1.665

Data Collection Statistics

Resolution limits40.00 - 2.95
the highest resolution shell value -
Completeness98.5
I/sigma(I)1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.5291

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0000932cellular_componentcytoplasmic mRNA processing body
A1990726cellular_componentLsm1-7-Pat1 complex
A0005845cellular_componentmRNA cap binding complex
A0005634cellular_componentnucleus
A0003682molecular_functionchromatin binding
A0003729molecular_functionmRNA binding
A0000339molecular_functionRNA cap binding
A0000290biological_processdeadenylation-dependent decapping of nuclear-transcribed mRNA
A0006397biological_processmRNA processing
A0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
H0005737cellular_componentcytoplasm
H0000932cellular_componentcytoplasmic mRNA processing body
H1990726cellular_componentLsm1-7-Pat1 complex
H0005845cellular_componentmRNA cap binding complex
H0005634cellular_componentnucleus
H0003682molecular_functionchromatin binding
H0003729molecular_functionmRNA binding
H0000339molecular_functionRNA cap binding
H0000290biological_processdeadenylation-dependent decapping of nuclear-transcribed mRNA
H0006397biological_processmRNA processing
H0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
B0071013cellular_componentcatalytic step 2 spliceosome
B0000932cellular_componentcytoplasmic mRNA processing body
B1990726cellular_componentLsm1-7-Pat1 complex
B0005730cellular_componentnucleolus
B0071011cellular_componentprecatalytic spliceosome
B0005732cellular_componentsmall nucleolar ribonucleoprotein complex
B0046540cellular_componentU4/U6 x U5 tri-snRNP complex
B0005688cellular_componentU6 snRNP
B0003723molecular_functionRNA binding
B0000398biological_processmRNA splicing, via spliceosome
B0006364biological_processrRNA processing
B0008033biological_processtRNA processing
I0071013cellular_componentcatalytic step 2 spliceosome
I0000932cellular_componentcytoplasmic mRNA processing body
I1990726cellular_componentLsm1-7-Pat1 complex
I0005730cellular_componentnucleolus
I0071011cellular_componentprecatalytic spliceosome
I0005732cellular_componentsmall nucleolar ribonucleoprotein complex
I0046540cellular_componentU4/U6 x U5 tri-snRNP complex
I0005688cellular_componentU6 snRNP
I0003723molecular_functionRNA binding
I0000398biological_processmRNA splicing, via spliceosome
I0006364biological_processrRNA processing
I0008033biological_processtRNA processing
C0071013cellular_componentcatalytic step 2 spliceosome
C0000932cellular_componentcytoplasmic mRNA processing body
C1990726cellular_componentLsm1-7-Pat1 complex
C0005730cellular_componentnucleolus
C0071011cellular_componentprecatalytic spliceosome
C0005732cellular_componentsmall nucleolar ribonucleoprotein complex
C0046540cellular_componentU4/U6 x U5 tri-snRNP complex
C0005688cellular_componentU6 snRNP
C0003723molecular_functionRNA binding
C0033962biological_processcytoplasmic mRNA processing body assembly
C0000398biological_processmRNA splicing, via spliceosome
C0006364biological_processrRNA processing
C0008033biological_processtRNA processing
J0071013cellular_componentcatalytic step 2 spliceosome
J0000932cellular_componentcytoplasmic mRNA processing body
J1990726cellular_componentLsm1-7-Pat1 complex
J0005730cellular_componentnucleolus
J0071011cellular_componentprecatalytic spliceosome
J0005732cellular_componentsmall nucleolar ribonucleoprotein complex
J0046540cellular_componentU4/U6 x U5 tri-snRNP complex
J0005688cellular_componentU6 snRNP
J0003723molecular_functionRNA binding
J0033962biological_processcytoplasmic mRNA processing body assembly
J0000398biological_processmRNA splicing, via spliceosome
J0006364biological_processrRNA processing
J0008033biological_processtRNA processing
G0000932cellular_componentcytoplasmic mRNA processing body
G1990726cellular_componentLsm1-7-Pat1 complex
G0005730cellular_componentnucleolus
G0005732cellular_componentsmall nucleolar ribonucleoprotein complex
G0005681cellular_componentspliceosomal complex
G0046540cellular_componentU4/U6 x U5 tri-snRNP complex
G0005688cellular_componentU6 snRNP
G0017070molecular_functionU6 snRNA binding
G0033962biological_processcytoplasmic mRNA processing body assembly
G0000398biological_processmRNA splicing, via spliceosome
G0000956biological_processnuclear-transcribed mRNA catabolic process
G0006364biological_processrRNA processing
G0000245biological_processspliceosomal complex assembly
G0000387biological_processspliceosomal snRNP assembly
G0008033biological_processtRNA processing
N0000932cellular_componentcytoplasmic mRNA processing body
N1990726cellular_componentLsm1-7-Pat1 complex
N0005730cellular_componentnucleolus
N0005732cellular_componentsmall nucleolar ribonucleoprotein complex
N0005681cellular_componentspliceosomal complex
N0046540cellular_componentU4/U6 x U5 tri-snRNP complex
N0005688cellular_componentU6 snRNP
N0017070molecular_functionU6 snRNA binding
N0033962biological_processcytoplasmic mRNA processing body assembly
N0000398biological_processmRNA splicing, via spliceosome
N0000956biological_processnuclear-transcribed mRNA catabolic process
N0006364biological_processrRNA processing
N0000245biological_processspliceosomal complex assembly
N0000387biological_processspliceosomal snRNP assembly
N0008033biological_processtRNA processing
E1990726cellular_componentLsm1-7-Pat1 complex
E0005730cellular_componentnucleolus
E0005732cellular_componentsmall nucleolar ribonucleoprotein complex
E0005681cellular_componentspliceosomal complex
E0046540cellular_componentU4/U6 x U5 tri-snRNP complex
E0005688cellular_componentU6 snRNP
E0003723molecular_functionRNA binding
E0000398biological_processmRNA splicing, via spliceosome
E0000956biological_processnuclear-transcribed mRNA catabolic process
E0006364biological_processrRNA processing
E0008033biological_processtRNA processing
L1990726cellular_componentLsm1-7-Pat1 complex
L0005730cellular_componentnucleolus
L0005732cellular_componentsmall nucleolar ribonucleoprotein complex
L0005681cellular_componentspliceosomal complex
L0046540cellular_componentU4/U6 x U5 tri-snRNP complex
L0005688cellular_componentU6 snRNP
L0003723molecular_functionRNA binding
L0000398biological_processmRNA splicing, via spliceosome
L0000956biological_processnuclear-transcribed mRNA catabolic process
L0006364biological_processrRNA processing
L0008033biological_processtRNA processing
D0000932cellular_componentcytoplasmic mRNA processing body
D1990726cellular_componentLsm1-7-Pat1 complex
D0005730cellular_componentnucleolus
D0005732cellular_componentsmall nucleolar ribonucleoprotein complex
D0005681cellular_componentspliceosomal complex
D0046540cellular_componentU4/U6 x U5 tri-snRNP complex
D0005688cellular_componentU6 snRNP
D0003723molecular_functionRNA binding
D0030490biological_processmaturation of SSU-rRNA
D0000398biological_processmRNA splicing, via spliceosome
D0008033biological_processtRNA processing
K0000932cellular_componentcytoplasmic mRNA processing body
K1990726cellular_componentLsm1-7-Pat1 complex
K0005730cellular_componentnucleolus
K0005732cellular_componentsmall nucleolar ribonucleoprotein complex
K0005681cellular_componentspliceosomal complex
K0046540cellular_componentU4/U6 x U5 tri-snRNP complex
K0005688cellular_componentU6 snRNP
K0003723molecular_functionRNA binding
K0030490biological_processmaturation of SSU-rRNA
K0000398biological_processmRNA splicing, via spliceosome
K0008033biological_processtRNA processing
F0071013cellular_componentcatalytic step 2 spliceosome
F0005737cellular_componentcytoplasm
F1990726cellular_componentLsm1-7-Pat1 complex
F0005730cellular_componentnucleolus
F0005732cellular_componentsmall nucleolar ribonucleoprotein complex
F0005689cellular_componentU12-type spliceosomal complex
F0071004cellular_componentU2-type prespliceosome
F0046540cellular_componentU4/U6 x U5 tri-snRNP complex
F0005688cellular_componentU6 snRNP
F0003723molecular_functionRNA binding
F0030490biological_processmaturation of SSU-rRNA
F0000398biological_processmRNA splicing, via spliceosome
F0000956biological_processnuclear-transcribed mRNA catabolic process
F0008033biological_processtRNA processing
M0071013cellular_componentcatalytic step 2 spliceosome
M0005737cellular_componentcytoplasm
M1990726cellular_componentLsm1-7-Pat1 complex
M0005730cellular_componentnucleolus
M0005732cellular_componentsmall nucleolar ribonucleoprotein complex
M0005689cellular_componentU12-type spliceosomal complex
M0071004cellular_componentU2-type prespliceosome
M0046540cellular_componentU4/U6 x U5 tri-snRNP complex
M0005688cellular_componentU6 snRNP
M0003723molecular_functionRNA binding
M0030490biological_processmaturation of SSU-rRNA
M0000398biological_processmRNA splicing, via spliceosome
M0000956biological_processnuclear-transcribed mRNA catabolic process
M0008033biological_processtRNA processing
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC12BINDING SITE FOR RESIDUE CL B 101
ChainResidue
BMSE1
BPHE4

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb4m75.ent.gz (416.11 KB)
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all (no-compress)pdb4m75.ent (1.59 MB)
header onlypdb4m75.ent.gz (16.49 KB)
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PDBx/mmCIF4m75.cif.gz (494.65 KB)
PDBMLall4m75.xml.gz (766.41 KB)
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no-atom4m75-noatom.xml.gz (65.94 KB)
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ext-atom4m75-extatom.xml.gz (221.12 KB)
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PDBMLplusall4m75-plus.xml.gz (769.69 KB)
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no-atom4m75-plus-noatom.xml.gz (69.22 KB)
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add only4m75-add.xml.gz (3.28 KB)
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RDF4m75.rdf.gz (128.7 KB)
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Structure factorsr4m75sf.ent.gz (1.48 MB)
Biological unit (PDB format)4m75.pdb1.gz (207.2 KB) (A,B,G,C,D,...)
*author and software defined assembly, 7 molecule(s) (heptameric)
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4m75.pdb2.gz (200.25 KB) (H,I,N,J,K,...)
*author and software defined assembly, 7 molecule(s) (heptameric)
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Validation reportsPDF4m75​_validation.pdf.gz (379.32 KB)
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PDF-full4m75​_full​_validation.pdf.gz (491.51 KB)
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XML4m75​_validation.xml.gz (61.44 KB)
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PNG4m75​_multipercentile​_validation.png.gz (158.75 KB)
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SVG4m75​_multipercentile​_validation.svg.gz (947 B)
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Sequence (fasta)4m75​_seq.txt
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