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- PDB-4c8q: Crystal structure of the yeast Lsm1-7-Pat1 complex -

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Basic information

Entry
Database: PDB / ID: 4c8q
TitleCrystal structure of the yeast Lsm1-7-Pat1 complex
Components
  • (U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN ...) x 6
  • DNA TOPOISOMERASE 2-ASSOCIATED PROTEIN PAT1
  • SM-LIKE PROTEIN LSM1
KeywordsTRANSCRIPTION / MRNA DECAPPING / SM FOLD / MRNA DEGRADATION
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 / spliceosomal tri-snRNP complex / P-body assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...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 / spliceosomal tri-snRNP complex / P-body assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of translational initiation / 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 / negative regulation of translational initiation / maturation of SSU-rRNA / spliceosomal complex / P-body / mRNA splicing, via spliceosome / kinetochore / mRNA processing / cytoplasmic stress granule / rRNA processing / cytosolic small ribosomal subunit / ribonucleoprotein complex / cell division / mRNA binding / chromatin binding / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
Sm-like protein Lsm1 / mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1 / 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 ...Sm-like protein Lsm1 / mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1 / 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
: / Deadenylation-dependent mRNA-decapping factor PAT1 / LSM complex subunit LSM2 / LSM complex subunit LSM4 / LSM complex subunit LSM5 / LSM1-LSM7 complex subunit LSM1 / LSM complex subunit LSM7 / LSM complex subunit LSM3 / LSM complex subunit LSM6
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.698 Å
AuthorsSharif, H. / Conti, E.
CitationJournal: Cell Rep. / Year: 2013
Title: Architecture of the Lsm1-7-Pat1 Complex: A Conserved Assembly in Eukaryotic Mrna Turnover
Authors: Sharif, H. / Conti, E.
History
DepositionOct 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SM-LIKE PROTEIN LSM1
B: U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2
C: U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3
D: U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4
E: U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5
F: U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6
G: U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7
H: DNA TOPOISOMERASE 2-ASSOCIATED PROTEIN PAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,14610
Polymers118,0298
Non-polymers1182
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13930 Å2
ΔGint-95.1 kcal/mol
Surface area49770 Å2
MethodPQS
Unit cell
Length a, b, c (Å)258.687, 258.687, 47.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 2 types, 2 molecules AH

#1: Protein SM-LIKE PROTEIN LSM1 / SPB8 PROTEIN / LSM1


Mass: 11935.651 Da / Num. of mol.: 1 / Fragment: RESIDUES 45-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P47017
#8: 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 / PAT 1


Mass: 37934.699 Da / Num. of mol.: 1 / Fragment: RESIDUES 456-783
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25644

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U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN ... , 6 types, 6 molecules BCDEFG

#2: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2 / SMALL NUCLEAR RIBONUCLEOPROTEIN D HOMOLOG SNP3 / LSM2


Mass: 12216.880 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P38203
#3: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3 / SMX4 PROTEIN / LSM3


Mass: 10039.262 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P57743
#4: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 / LSM4


Mass: 13035.543 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40070
#5: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5 / LSM5


Mass: 10432.954 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40089
#6: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6 / LSM6


Mass: 9406.579 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q06406
#7: Protein U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7 / LSM7


Mass: 13027.045 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53905

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Non-polymers , 1 types, 2 molecules

#9: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.39 %
Description: CHIMERIC MODEL WAS MADE FOR MOLECULAR REPLACEMENT
Crystal growDetails: 100 MM HEPES PH 7.0, 20% MPD, 10 MM HEXAMINE COBALT(III) CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 3.7→84.68 Å / Num. obs: 36441 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 133.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.4 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C92

4c92


Resolution: 3.698→43.42 Å / SU ML: 0.67 / σ(F): 39.43 / Phase error: 31.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2954 1813 5 %
Rwork0.249 --
obs0.2513 36400 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 129.27 Å2
Refinement stepCycle: LAST / Resolution: 3.698→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6278 0 2 0 6280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066353
X-RAY DIFFRACTIONf_angle_d1.5338638
X-RAY DIFFRACTIONf_dihedral_angle_d15.4292143
X-RAY DIFFRACTIONf_chiral_restr0.0581070
X-RAY DIFFRACTIONf_plane_restr0.0061103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6983-3.79830.46361190.38912261X-RAY DIFFRACTION82
3.7983-3.910.33311400.34922583X-RAY DIFFRACTION92
3.91-4.03610.33951390.32422663X-RAY DIFFRACTION99
4.0361-4.18020.31511430.28452712X-RAY DIFFRACTION99
4.1802-4.34740.31241440.25492730X-RAY DIFFRACTION99
4.3474-4.54510.2811480.23282711X-RAY DIFFRACTION99
4.5451-4.78440.25361470.20662764X-RAY DIFFRACTION99
4.7844-5.08380.2921440.21512706X-RAY DIFFRACTION99
5.0838-5.47560.30151360.2552733X-RAY DIFFRACTION99
5.4756-6.02530.3591490.28442766X-RAY DIFFRACTION99
6.0253-6.89420.29721400.29462708X-RAY DIFFRACTION99
6.8942-8.67460.26651390.23842657X-RAY DIFFRACTION97
8.6746-43.42320.26651250.2072593X-RAY DIFFRACTION93

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