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- PDB-5vsu: Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA -

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Basic information

Entry
Database: PDB / ID: 5vsu
TitleStructure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA
Components
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • Saccharomyces cerevisiae strain T8 chromosome XII sequence
  • U4/U6 snRNA-associated-splicing factor PRP24
KeywordsSPLICING / Lsm2-8 spliceosome U6 Prp24
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 / snRNA binding / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / P-body assembly / U2-type prespliceosome ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / snRNA binding / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / P-body assembly / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / 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 / spliceosomal complex / maturation of SSU-rRNA / P-body / mRNA splicing, via spliceosome / rRNA processing / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction motif / Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 ...Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction motif / Sm-like protein Lsm8 / 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 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / SH3 type barrels. / Roll / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / LSM complex subunit LSM2 / LSM complex subunit LSM4 / LSM complex subunit LSM5 / LSM2-LSM8 complex subunit LSM8 / U4/U6 snRNA-associated-splicing factor PRP24 / 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: 3.1 Å
AuthorsMontemayor, E.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM065166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118131 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118075 United States
CitationJournal: Nat Commun / Year: 2018
Title: Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.
Authors: Montemayor, E.J. / Didychuk, A.L. / Yake, A.D. / Sidhu, G.K. / Brow, D.A. / Butcher, S.E.
History
DepositionMay 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U4/U6 snRNA-associated-splicing factor PRP24
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: U6 snRNA-associated Sm-like protein LSm8
I: Saccharomyces cerevisiae strain T8 chromosome XII sequence


Theoretical massNumber of molelcules
Total (without water)157,4749
Polymers157,4749
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26130 Å2
ΔGint-144 kcal/mol
Surface area54000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.157, 114.728, 179.844
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules BCDEFGH

#2: Protein U6 snRNA-associated Sm-like protein LSm2 / Small nuclear ribonucleoprotein D homolog SNP3


Mass: 11453.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LSM2, SMX5, SNP3, YBL026W, YBL0425 / Production host: Escherichia coli (E. coli) / References: UniProt: P38203
#3: Protein U6 snRNA-associated Sm-like protein LSm3 / SmX4 protein


Mass: 10314.587 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LSM3, SMX4, USS2, YLR438C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P57743
#4: Protein U6 snRNA-associated Sm-like protein LSm4


Mass: 10902.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LSM4, SDB23, USS1, YER112W / Production host: Escherichia coli (E. coli) / References: UniProt: P40070
#5: Protein U6 snRNA-associated Sm-like protein LSm5


Mass: 10708.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LSM5, YER146W / Production host: Escherichia coli (E. coli) / References: UniProt: P40089
#6: Protein U6 snRNA-associated Sm-like protein LSm6


Mass: 9550.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LSM6, YDR378C, D9481.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06406
#7: Protein U6 snRNA-associated Sm-like protein LSm7


Mass: 13302.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LSM7, YNL147W, N1202, N1780 / Production host: Escherichia coli (E. coli) / References: UniProt: P53905
#8: Protein U6 snRNA-associated Sm-like protein LSm8


Mass: 12547.507 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LSM8, YJR022W, J1464, YJR83.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P47093

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Protein / RNA chain , 2 types, 2 molecules AI

#1: Protein U4/U6 snRNA-associated-splicing factor PRP24 / U4/U6 snRNP protein


Mass: 51998.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PRP24, YMR268C, YM8156.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P49960
#9: RNA chain Saccharomyces cerevisiae strain T8 chromosome XII sequence


Mass: 26695.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: GenBank: 1039023528

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M NH4F 0.1 M HEPES pH 7.4 0.01 M MgCl2 18 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→96.723 Å / Num. obs: 27164 / % possible obs: 100 % / Redundancy: 51.2 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 13
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 47.7 % / Rmerge(I) obs: 4.031 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata scaling
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→96.723 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 36.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2982 3783 7.45 %
Rwork0.2339 --
obs0.2386 50793 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→96.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7681 1555 4 0 9240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119517
X-RAY DIFFRACTIONf_angle_d1.66713166
X-RAY DIFFRACTIONf_dihedral_angle_d13.3395660
X-RAY DIFFRACTIONf_chiral_restr0.0831597
X-RAY DIFFRACTIONf_plane_restr0.011398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13930.491370.46391733X-RAY DIFFRACTION100
3.1393-3.18060.48631460.44421800X-RAY DIFFRACTION100
3.1806-3.22410.45511400.43921731X-RAY DIFFRACTION100
3.2241-3.27020.41011390.41971726X-RAY DIFFRACTION100
3.2702-3.3190.45531360.44561735X-RAY DIFFRACTION100
3.319-3.37090.46841400.40861798X-RAY DIFFRACTION100
3.3709-3.42610.45581360.41811667X-RAY DIFFRACTION99
3.4261-3.48520.42721430.39481792X-RAY DIFFRACTION100
3.4852-3.54860.38561340.3571703X-RAY DIFFRACTION99
3.5486-3.61690.3411430.33131744X-RAY DIFFRACTION100
3.6169-3.69070.3321440.32381788X-RAY DIFFRACTION100
3.6907-3.77090.43961330.33571660X-RAY DIFFRACTION100
3.7709-3.85870.37721490.35031781X-RAY DIFFRACTION99
3.8587-3.95520.43721330.33461702X-RAY DIFFRACTION98
3.9552-4.06210.30561410.26661741X-RAY DIFFRACTION100
4.0621-4.18160.25561420.23091726X-RAY DIFFRACTION100
4.1816-4.31660.32831400.22021765X-RAY DIFFRACTION100
4.3166-4.47090.21911380.19131727X-RAY DIFFRACTION100
4.4709-4.64990.23141410.18211772X-RAY DIFFRACTION100
4.6499-4.86150.21461360.1631716X-RAY DIFFRACTION100
4.8615-5.11780.2481440.16511753X-RAY DIFFRACTION100
5.1178-5.43840.2551410.18921743X-RAY DIFFRACTION100
5.4384-5.85830.2591470.1891750X-RAY DIFFRACTION100
5.8583-6.44770.28151390.20491742X-RAY DIFFRACTION100
6.4477-7.38040.27661350.20161721X-RAY DIFFRACTION100
7.3804-9.29740.27881440.19621736X-RAY DIFFRACTION100
9.2974-96.76990.27891420.18931758X-RAY DIFFRACTION100

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