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- PDB-3swn: Structure of the LSm657 Complex: An Assembly Intermediate of the ... -

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Basic information

Entry
Database: PDB / ID: 3swn
TitleStructure of the LSm657 Complex: An Assembly Intermediate of the LSm1 7 and LSm2 8 Rings
Components
  • U6 snRNA-associated Sm-like protein LSm5
  • U6 snRNA-associated Sm-like protein LSm6
  • U6 snRNA-associated Sm-like protein LSm7
KeywordsRNA BINDING PROTEIN / Sm / rna metabolism / rna / nuclear
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / Lsm1-7-Pat1 complex / U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / poly(U) RNA binding / U2 snRNP ...mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / Lsm1-7-Pat1 complex / U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / poly(U) RNA binding / U2 snRNP / tRNA processing / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / telomerase holoenzyme complex assembly / U5 snRNP / U2 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / maturation of SSU-rRNA / spliceosomal complex / P-body / mRNA splicing, via spliceosome / rRNA processing / nucleolus / RNA binding / nucleus / cytosol
Similarity search - Function
Sm-like protein Lsm7 / Sm-like protein LSm5 / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. ...Sm-like protein Lsm7 / Sm-like protein LSm5 / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / 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
U6 snRNA-associated Sm-like protein LSm5 / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm6
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMund, M. / Neu, A. / Ullmann, J.L. / Neu, U. / Sprangers, R.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure of the LSm657 complex: an assembly intermediate of the LSm1-7 and LSm2-8 rings.
Authors: Mund, M. / Neu, A. / Ullmann, J. / Neu, U. / Sprangers, R.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: U6 snRNA-associated Sm-like protein LSm7
A: U6 snRNA-associated Sm-like protein LSm5
B: U6 snRNA-associated Sm-like protein LSm6
F: U6 snRNA-associated Sm-like protein LSm7
D: U6 snRNA-associated Sm-like protein LSm5
E: U6 snRNA-associated Sm-like protein LSm6
O: U6 snRNA-associated Sm-like protein LSm7
P: U6 snRNA-associated Sm-like protein LSm5
Q: U6 snRNA-associated Sm-like protein LSm6
R: U6 snRNA-associated Sm-like protein LSm7
S: U6 snRNA-associated Sm-like protein LSm5
T: U6 snRNA-associated Sm-like protein LSm6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,59428
Polymers121,54712
Non-polymers1,04716
Water43224
1
C: U6 snRNA-associated Sm-like protein LSm7
A: U6 snRNA-associated Sm-like protein LSm5
B: U6 snRNA-associated Sm-like protein LSm6
F: U6 snRNA-associated Sm-like protein LSm7
D: U6 snRNA-associated Sm-like protein LSm5
E: U6 snRNA-associated Sm-like protein LSm6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,29714
Polymers60,7746
Non-polymers5238
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-251 kcal/mol
Surface area18500 Å2
MethodPISA
2
O: U6 snRNA-associated Sm-like protein LSm7
P: U6 snRNA-associated Sm-like protein LSm5
Q: U6 snRNA-associated Sm-like protein LSm6
R: U6 snRNA-associated Sm-like protein LSm7
S: U6 snRNA-associated Sm-like protein LSm5
T: U6 snRNA-associated Sm-like protein LSm6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,29714
Polymers60,7746
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-257 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.530, 63.100, 92.760
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 18:24 or resseq 27:36 or resseq 42:51 or resseq 54:65 or resseq 70:75)
211chain P and (resseq 18:24 or resseq 27:36 or resseq 42:51 or resseq 54:65 or resseq 70:75)
112chain B and (resseq 16:22 or resseq 26:34 or resseq 40:49 or resseq 52:62 or resseq 67:72)
212chain Q and (resseq 16:22 or resseq 26:34 or resseq 40:49 or resseq 52:62 or resseq 67:72)
113chain C and (resseq 35:41 or resseq 45:53 or resseq 59:67 or resseq 75:88 or resseq 93:98)
213chain O and (resseq 35:41 or resseq 45:53 or resseq 59:67 or resseq 75:88 or resseq 93:98)
114chain D and (resseq 18:24 or resseq 27:36 or resseq 42:51 or resseq 54:65 or resseq 70:75)
214chain S and (resseq 18:24 or resseq 27:36 or resseq 42:51 or resseq 54:65 or resseq 70:75)
115chain E and (resseq 16:22 or resseq 26:34 or resseq 40:49 or resseq 52:62 or resseq 67:72)
215chain T and (resseq 16:22 or resseq 26:34 or resseq 40:49 or resseq 52:62 or resseq 67:72)
116chain F and (resseq 35:41 or resseq 45:53 or resseq 59:67 or resseq 75:88 or resseq 93:98)
216chain R and (resseq 35:41 or resseq 45:53 or resseq 59:67 or resseq 75:88 or resseq 93:98)

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
U6 snRNA-associated Sm-like protein LSm7


Mass: 12804.556 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: lsm7, SPCC285.12 / Production host: Escherichia coli (E. coli) / References: UniProt: O74499
#2: Protein
U6 snRNA-associated Sm-like protein LSm5


Mass: 9048.568 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: lsm5, SPBC20F10.09 / Production host: Escherichia coli (E. coli) / References: UniProt: O42978
#3: Protein
U6 snRNA-associated Sm-like protein LSm6


Mass: 8533.728 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: lsm6, SPAC2F3.17c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UUI1
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.91 Å3/Da / Density % sol: 35.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM zinc acetate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2010
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 62580 / Num. obs: 60656 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.56 Å / % possible all: 87.9

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Processing

Software
NameVersionClassification
go.comdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.38 Å / SU ML: 0.41 / σ(F): 0.81 / Phase error: 31.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2691 3095 5.1 %
Rwork0.2182 --
obs0.2209 60648 96.93 %
all-62580 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.844 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.859 Å20 Å2-0.0136 Å2
2--5.7509 Å20 Å2
3----2.892 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 16 24 6786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066820
X-RAY DIFFRACTIONf_angle_d1.0329193
X-RAY DIFFRACTIONf_dihedral_angle_d16.0782551
X-RAY DIFFRACTIONf_chiral_restr0.0761095
X-RAY DIFFRACTIONf_plane_restr0.0041164
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A359X-RAY DIFFRACTIONPOSITIONAL
12P359X-RAY DIFFRACTIONPOSITIONAL0.038
21B344X-RAY DIFFRACTIONPOSITIONAL
22Q344X-RAY DIFFRACTIONPOSITIONAL0.039
31C335X-RAY DIFFRACTIONPOSITIONAL
32O335X-RAY DIFFRACTIONPOSITIONAL0.012
41D359X-RAY DIFFRACTIONPOSITIONAL
42S359X-RAY DIFFRACTIONPOSITIONAL0.012
51E344X-RAY DIFFRACTIONPOSITIONAL
52T344X-RAY DIFFRACTIONPOSITIONAL0.011
61F344X-RAY DIFFRACTIONPOSITIONAL
62R344X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53640.45591360.35472166X-RAY DIFFRACTION81
2.5364-2.57790.38311430.33112614X-RAY DIFFRACTION98
2.5779-2.62240.37031440.31122697X-RAY DIFFRACTION98
2.6224-2.67010.35581330.31922707X-RAY DIFFRACTION98
2.6701-2.72140.38491610.3112574X-RAY DIFFRACTION98
2.7214-2.7770.41171610.28882602X-RAY DIFFRACTION98
2.777-2.83730.3551330.3162666X-RAY DIFFRACTION97
2.8373-2.90330.33771340.29832602X-RAY DIFFRACTION97
2.9033-2.97590.34391280.28042675X-RAY DIFFRACTION98
2.9759-3.05640.34561480.2412646X-RAY DIFFRACTION98
3.0564-3.14630.29351290.22612668X-RAY DIFFRACTION98
3.1463-3.24780.32531390.2432630X-RAY DIFFRACTION98
3.2478-3.36390.31191150.22432693X-RAY DIFFRACTION98
3.3639-3.49850.23711320.22532668X-RAY DIFFRACTION98
3.4985-3.65770.25821490.19682620X-RAY DIFFRACTION98
3.6577-3.85040.25381630.222604X-RAY DIFFRACTION98
3.8504-4.09150.29091250.19912603X-RAY DIFFRACTION96
4.0915-4.40720.21681530.17552611X-RAY DIFFRACTION96
4.4072-4.85030.19861290.14122656X-RAY DIFFRACTION98
4.8503-5.55120.22481440.18262637X-RAY DIFFRACTION98
5.5512-6.990.2111310.23562635X-RAY DIFFRACTION97
6.99-46.3880.27451650.22532579X-RAY DIFFRACTION96

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