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- EMDB-8009: Combined Body and arm regions of the yeast spliceosomal U4/U6.U5 ... -

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Basic information

Entry
Database: EMDB / ID: 8009
TitleCombined Body and arm regions of the yeast spliceosomal U4/U6.U5 tri-snRNP by masked classification and refinement-Class 2
Map dataCombined body and arm regions of the yeast spliceosomal U4/U6.U5 tri-snRNP from masked classification and refinement-class2
Sampletri-snRNP complex with 30 proteins and 3 snRNA:
(nucleic-acidNucleic acid) x 3 / Prp8 / Prp4 / Prp6 / Dib1 / Prp31 / Prp3 / Brr2 / unknown proteins / SmB ...(nucleic-acidNucleic acid) x 3 / Prp8 / Prp4 / Prp6 / Dib1 / Prp31 / Prp3 / Brr2 / unknown proteins / SmB / U4 SmD1 / SmD2 / SmD3 / SmE / SmF / SmG / Snu66 / U5 SmE / U5 SmD1 / Snu13 / LSm2 / LSm3 / LSm4 / LSm5 / LSm6 / LSm7 / LSm8 / Snu114
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsNguyen THD / Galej WP / Bai X-C / Oubridge C / Newman AJ / Scheres SHW / Nagai K
CitationJournal: Nature / Year: 2016
Title: Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-Chen Bai / Chris Oubridge / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai
DateDeposition: Dec 14, 2015 / Header (metadata) release: Jan 20, 2016 / Map release: Mar 30, 2016 / Last update: Aug 30, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8009.map.gz (map file in CCP4 format, 219489 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
380 pix
1.43 Å/pix.
= 543.4 Å
380 pix
1.43 Å/pix.
= 543.4 Å
380 pix
1.43 Å/pix.
= 543.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.057787698 - 0.15609612
Average (Standard dev.)-5.312296E-6 (0.0044922824)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions380380380
Origin000
Limit379379379
Spacing380380380
CellA=B=C: 543.39996 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z543.400543.400543.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0580.156-0.000

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Supplemental data

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Sample components

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Entire tri-snRNP complex with 30 proteins and 3 snRNA

EntireName: tri-snRNP complex with 30 proteins and 3 snRNA / Number of components: 31
MassTheoretical: 1.5 MDa

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Component #1: protein, tri-snRNP complex with 30 proteins and 3 snRNA

ProteinName: tri-snRNP complex with 30 proteins and 3 snRNA / Recombinant expression: No
MassTheoretical: 1.5 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: nucleic-acid, U4 snRNA

Nucleic-acidName: U4 snRNAU4 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCCUUAUGC ACGGGAAAUA CGCAUAUCAG UGAGGAUUCG UCCGAGAUUG UGUUUUUGCU GGUUGAAAUU UAAUUAUAAA CCAGACCGUC UCCUCAUGGU CAAUUCGGUG UUCGCUUUUG AAUACUUCAA GACUAUGUAG GGAAUUUUUG GAAUACCUUU
MassTheoretical: 39.813488 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #3: nucleic-acid, U6 snRNA

Nucleic-acidName: U6 snRNAU6 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUCGCGAAG UAACCCUUCG UGGACAUUUG GUCAAUUUGA AACAAUACAG AGAUGAUCAG CAGUUCCCCU GCAUAAGGAU GAACCGUUUU ACAAAGAGAU UUAUUUCGUU UU
MassTheoretical: 25.635123 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #4: protein, Prp8

ProteinName: Prp8 / Recombinant expression: No
MassTheoretical: 255.921422 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #5: protein, Prp4

ProteinName: Prp4 / Recombinant expression: No
MassTheoretical: 39.953031 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #6: protein, Prp6

ProteinName: Prp6 / Recombinant expression: No
MassTheoretical: 84.644094 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #7: protein, Dib1

ProteinName: Dib1 / Recombinant expression: No
MassTheoretical: 16.480982 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #8: protein, Prp31

ProteinName: Prp31 / Recombinant expression: No
MassTheoretical: 47.128652 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #9: protein, Prp3

ProteinName: Prp3 / Recombinant expression: No
MassTheoretical: 37.87025 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #10: protein, Brr2

ProteinName: Brr2 / Recombinant expression: No
MassTheoretical: 202.6655 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #11: protein, unknown proteins

ProteinName: unknown proteins / Recombinant expression: No
MassTheoretical: 8.528504 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #12: protein, SmB

ProteinName: SmB / Recombinant expression: No
MassTheoretical: 9.183853 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #13: protein, U4 SmD1

ProteinName: U4 SmD1 / Recombinant expression: No
MassTheoretical: 10.327998 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #14: protein, SmD2

ProteinName: SmD2 / Recombinant expression: No
MassTheoretical: 11.021953 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #15: protein, SmD3

ProteinName: SmD3 / Recombinant expression: No
MassTheoretical: 9.011384 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #16: protein, SmE

ProteinName: SmE / Recombinant expression: No
MassTheoretical: 8.320758 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #17: protein, SmF

ProteinName: SmF / Recombinant expression: No
MassTheoretical: 8.178299 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #18: protein, SmG

ProteinName: SmG / Recombinant expression: No
MassTheoretical: 7.662906 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #19: protein, Snu66

ProteinName: Snu66 / Recombinant expression: No
MassTheoretical: 24.367936 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #20: protein, U5 SmE

ProteinName: U5 SmE / Recombinant expression: No
MassTheoretical: 8.362859 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #21: protein, U5 SmD1

ProteinName: U5 SmD1 / Recombinant expression: No
MassTheoretical: 9.200678 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #22: nucleic-acid, U5 snRNA

Nucleic-acidName: U5 snRNAU5 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAGCAGCUUU ACAGAUCAAU GGCGGAGGGA GGUCAACAUC AAGAACUGUG GGCCUUUUAU UGCCUAUAGA ACUUAUAACG AACAUGGUUC UUGCCUUUUA CCAGAACCAU CCGGGUGUUG UCUCCAUAGA AACAGGUAAA GCUGUCCGUU ACUGUGGGCU UGCCAUAUUU UUUGGAACUU UUCUGCCCUU UUUCUCAAUG AGUAAGGAGG GCGU
MassTheoretical: 45.305805 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #23: protein, Snu13

ProteinName: Snu13 / Recombinant expression: No
MassTheoretical: 13.364584 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #24: protein, LSm2

ProteinName: LSm2 / Recombinant expression: No
MassTheoretical: 10.530101 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #25: protein, LSm3

ProteinName: LSm3 / Recombinant expression: No
MassTheoretical: 8.747967 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #26: protein, LSm4

ProteinName: LSm4 / Recombinant expression: No
MassTheoretical: 8.594071 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #27: protein, LSm5

ProteinName: LSm5 / Recombinant expression: No
MassTheoretical: 8.458736 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #28: protein, LSm6

ProteinName: LSm6 / Recombinant expression: No
MassTheoretical: 8.227233 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #29: protein, LSm7

ProteinName: LSm7 / Recombinant expression: No
MassTheoretical: 7.233692 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #30: protein, LSm8

ProteinName: LSm8 / Recombinant expression: No
MassTheoretical: 7.1935 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #31: protein, Snu114

ProteinName: Snu114 / Recombinant expression: No
MassTheoretical: 97.172828 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 38 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000 X (nominal), 35714 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 3500 nm / Energy filter: GIF Quantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 26367
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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