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- PDB-5gao: Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP -

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Database: PDB / ID: 5gao
TitleHead region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Components
  • (Pre-mRNA-splicing ...) x 2
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequence
  • Small nuclear ribonucleoprotein-associated protein B
  • Snu66
KeywordsTRANSCRIPTION / pre-mRNA splicing / snRNP / GTPase / spliceosome
Function / homology
Function and homology information


maturation of 5S rRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome ...maturation of 5S rRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / commitment complex / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / RNA helicase activity / nucleic acid binding / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Cytidine Deaminase, domain 2 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain ...Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Cytidine Deaminase, domain 2 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Cytidine Deaminase; domain 2 / Small nuclear ribonucleoprotein Sm D3 / Sec63 domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / C2 domain / LSM domain superfamily / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Helicase conserved C-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / DNA polymerase; domain 1 / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Ribonuclease H-like superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D1 ...: / RNA / RNA (> 10) / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 4.2 Å
AuthorsNguyen, T.H.D. / Galej, W.P. / Bai, X.C. / Oubridge, C. / Scheres, S.H.W. / Newman, A.J. / Nagai, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Citation
Journal: 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 /
Abstract: U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led ...U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.
#1: Journal: Nature / Year: 2015
Title: The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-chen Bai / Christos G Savva / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
Abstract: U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key ...U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 Å resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: em_imaging_optics / em_software ...em_imaging_optics / em_software / pdbx_audit_support / struct_conn
Item: _em_imaging_optics.energyfilter_name / _em_software.name ..._em_imaging_optics.energyfilter_name / _em_software.name / _em_software.version / _pdbx_audit_support.funding_organization
Revision 1.3Oct 3, 2018Group: Data collection / Refinement description
Category: refine / refine_hist ...refine / refine_hist / refine_ls_restr / refine_ls_shell
Item: _refine.pdbx_refine_id / _refine_hist.pdbx_refine_id ..._refine.pdbx_refine_id / _refine_hist.pdbx_refine_id / _refine_ls_restr.pdbx_refine_id / _refine_ls_shell.pdbx_refine_id
Revision 1.4Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c

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Structure visualization

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Assembly

Deposited unit
k: Small nuclear ribonucleoprotein-associated protein B
l: Small nuclear ribonucleoprotein Sm D1
m: Small nuclear ribonucleoprotein Sm D2
n: Small nuclear ribonucleoprotein Sm D3
p: Small nuclear ribonucleoprotein E
q: Small nuclear ribonucleoprotein F
r: Small nuclear ribonucleoprotein G
E: Snu66
B: Pre-mRNA-splicing helicase BRR2
V: Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequence
A: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)423,78211
Polymers423,78211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35630 Å2
ΔGint-169 kcal/mol
Surface area132600 Å2
MethodPISA

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Components

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Protein , 2 types, 2 molecules kE

#1: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB


Mass: 22426.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The SmB protein from the U4 snRNP Sm protein ring. The C-terminus is disordered in this and other previously reported structures.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P40018
#8: Protein Snu66


Mass: 25078.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NB: Snu66 protein has been mostly fitted as poly(Ala) into helices and extended polypeptide within the EM map. The authors do not believe the numbering to be accurate and it is likely incorrect.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q12420*PLUS

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Small nuclear ribonucleoprotein ... , 6 types, 6 molecules lmnpqr

#2: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


Mass: 16296.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The SmD1 protein from the U4 snRNP Sm protein ring.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q02260
#3: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 12876.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The SmD2 protein from the U4 snRNP Sm protein ring.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q06217
#4: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3 / U4 SmD3


Mass: 11240.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The SmD3 protein from the U4 snRNP Sm protein ring.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P43321
#5: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10385.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The SmE protein from the U4 snRNP Sm protein ring. / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q12330
#6: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / U4 SmF


Mass: 9669.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The SmF protein from the U4 snRNP Sm protein ring. / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P54999
#7: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / U4 SmG


Mass: 8490.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The SmG protein from the U4 snRNP Sm protein ring. / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P40204

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Pre-mRNA-splicing ... , 2 types, 2 molecules BA

#9: Protein Pre-mRNA-splicing helicase BRR2 / Protein Snu246 / Brr2 RNA helicase


Mass: 246470.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Brr2 RNA helicase loaded onto U4 snRNA strand of the U4/U6 duplex between Stem 1 duplex and the 3' stem loop.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P32639, RNA helicase
#11: Protein Pre-mRNA-splicing factor 8 / Prp8 Jab1/MPN domain


Mass: 30231.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Prp8 Jab1/MPN domain is connected to the rest of the Prp8 protein by a flexible linker peptide.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P33334

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RNA chain , 1 types, 1 molecules V

#10: RNA chain Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequence


Mass: 30615.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: This U4 snRNA region has a disordered region between stem 1 of the U4/U6 snRNA duplex and where the RNA is loaded into Brr2 protein. The apical part of the 3' stem loop and the region ...Details: This U4 snRNA region has a disordered region between stem 1 of the U4/U6 snRNA duplex and where the RNA is loaded into Brr2 protein. The apical part of the 3' stem loop and the region following the Sm site are also disordered.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: GenBank: 807071957

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.40 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123
Buffer solutionpH: 7.9
Buffer componentConc.: 1 mM / Name: DTT
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportDetails: Grids are made of holey carbon, carbon-coated and glow discharged in N-amylamine.
Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Calibrated magnification: 35714 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 2 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 16 sec. / Electron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2477
EM imaging opticsEnergyfilter name: GIF Quantum
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

SoftwareName: REFMAC / Version: 5.8.0124 / Classification: refinement
EM software
IDNameVersionCategory
1RELIONparticle selection
2DigitalMicrographimage acquisition
4CTFFIND4CTF correction
7Coot0.8.3model fitting
9REFMAC5.8model refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 473827
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140155 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDPdb chain residue range
14BGD

4bgd

B1442-2163
24BGD

4bgd

A12143-2396
RefinementResolution: 3.6→154.44 Å / Cor.coef. Fo:Fc: 0.967 / SU B: 47.302 / SU ML: 0.6 / ESU R: 0.774
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.31528 --
obs0.31528 141936 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 379.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å24.49 Å20.78 Å2
2--1.53 Å22.47 Å2
3----1.94 Å2
Refinement stepCycle: 1 / Total: 23074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01923612
ELECTRON MICROSCOPYr_bond_other_d0.0020.0222280
ELECTRON MICROSCOPYr_angle_refined_deg1.3011.91232285
ELECTRON MICROSCOPYr_angle_other_deg0.96351151
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.7825.2653081
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.00224.624917
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.557153715
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.67715105
ELECTRON MICROSCOPYr_chiral_restr0.0770.23771
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0225887
ELECTRON MICROSCOPYr_gen_planes_other0.0020.025267
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it21.10737.24411441
ELECTRON MICROSCOPYr_mcbond_other21.09937.24511440
ELECTRON MICROSCOPYr_mcangle_it33.98455.75214251
ELECTRON MICROSCOPYr_mcangle_other33.98355.75214252
ELECTRON MICROSCOPYr_scbond_it21.11438.88212171
ELECTRON MICROSCOPYr_scbond_other21.09838.88412169
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other36.32957.63918033
ELECTRON MICROSCOPYr_long_range_B_refined49.73634449
ELECTRON MICROSCOPYr_long_range_B_other49.73534450
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork3.956 10577 -
Rfree-0 -
obs--100 %

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