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- PDB-5zwn: Cryo-EM structure of the yeast pre-B complex at an average resolu... -

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Entry
Database: PDB / ID: 5zwn
TitleCryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region)
Components
  • (Small nuclear ribonucleoprotein ...) x 6
  • (U1 small nuclear ribonucleoprotein ...) x 5
  • 56 kDa U1 small nuclear ribonucleoprotein component
  • Pre-mRNA-processing factor 39
  • Pre-mRNA-splicing ATP-dependent RNA helicase PRP28
  • Protein LUC7
  • Protein NAM8
  • Small nuclear ribonucleoprotein-associated protein B
  • U1 snRNA
  • U1 snRNP
  • pre-mRNA
KeywordsSPLICING / spliceosme / assemply / pre-B complex / U1 snRNP
Function / homology
Function and homology information


first spliceosomal transesterification activity / mRNA splice site recognition / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / snRNP binding / small nuclear ribonucleoprotein complex / splicing factor binding / SMN-Sm protein complex ...first spliceosomal transesterification activity / mRNA splice site recognition / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / snRNP binding / small nuclear ribonucleoprotein complex / splicing factor binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / commitment complex / U2-type prespliceosome assembly / U2 snRNP / U1 snRNP / U4 snRNP / U2-type prespliceosome / poly(U) RNA binding / pre-mRNA 5'-splice site binding / precatalytic spliceosome / mRNA 5'-splice site recognition / spliceosomal complex assembly / Prp19 complex / U5 snRNP / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / Luc7-related / LUC7 N_terminus / Snu56-like U1 small nuclear ribonucleoprotein component / Snu56-like U1 small nuclear ribonucleoprotein component / SNU71 RNA binding domain / SNU71 N-terminal / U1 small nuclear ribonucleoprotein C / PRP39 C-terminal HAT repeat / U1 small nuclear ribonucleoprotein of 70kDa N-terminal ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / Luc7-related / LUC7 N_terminus / Snu56-like U1 small nuclear ribonucleoprotein component / Snu56-like U1 small nuclear ribonucleoprotein component / SNU71 RNA binding domain / SNU71 N-terminal / U1 small nuclear ribonucleoprotein C / PRP39 C-terminal HAT repeat / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / : / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / : / U1-C, C2H2-type zinc finger / U1 zinc finger / PWI domain / PWI, domain in splicing factors / PRP39 N-terminal HAT repeat / : / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / SH3 type barrels. - #100 / Small nuclear ribonucleoprotein Sm D2 / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Small nuclear ribonucleoprotein Sm D3 / 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 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / : / Sm domain profile. / DEAD-box RNA helicase Q motif profile. / LSM domain superfamily / RRM (RNA recognition motif) domain / Zinc finger C2H2 superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / SH3 type barrels. / Helicase conserved C-terminal domain / Tetratricopeptide-like helical domain superfamily / helicase superfamily c-terminal domain / 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 / Roll / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 / U1 small nuclear ribonucleoprotein A / Pre-mRNA-processing factor 39 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U1 small nuclear ribonucleoprotein component SNU71 ...RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 / U1 small nuclear ribonucleoprotein A / Pre-mRNA-processing factor 39 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U1 small nuclear ribonucleoprotein component SNU71 / Small nuclear ribonucleoprotein F / Protein NAM8 / U1 small nuclear ribonucleoprotein 70 kDa homolog / Small nuclear ribonucleoprotein Sm D1 / U1 small nuclear ribonucleoprotein component PRP42 / 56 kDa U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein C / Small nuclear ribonucleoprotein Sm D2 / Protein LUC7 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBai, R. / Wan, R. / Yan, C. / Lei, J. / Shi, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31430020 China
National Natural Science Foundation of China31621092 China
Ministry of Science and Technology (China)2016YFA0501100 China
CitationJournal: Science / Year: 2018
Title: Structures of the fully assembled spliceosome before activation.
Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Jianlin Lei / Yigong Shi /
Abstract: The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 ...The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.
History
DepositionMay 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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.Z_PDB
Revision 1.2Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _refine.ls_d_res_high / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

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Assembly

Deposited unit
G: pre-mRNA
P: U1 snRNA
Q: U1 small nuclear ribonucleoprotein 70 kDa homolog
R: U1 small nuclear ribonucleoprotein C
S: U1 small nuclear ribonucleoprotein A
T: U1 small nuclear ribonucleoprotein component PRP42
U: Pre-mRNA-processing factor 39
V: Protein NAM8
W: 56 kDa U1 small nuclear ribonucleoprotein component
a: Small nuclear ribonucleoprotein-associated protein B
b: Small nuclear ribonucleoprotein Sm D1
c: Small nuclear ribonucleoprotein Sm D2
d: Small nuclear ribonucleoprotein Sm D3
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
X: U1 small nuclear ribonucleoprotein component SNU71
Y: Protein LUC7
x: U1 snRNP
y: Pre-mRNA-splicing ATP-dependent RNA helicase PRP28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)802,38323
Polymers802,18720
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules GP

#1: RNA chain pre-mRNA


Mass: 7130.372 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#2: RNA chain U1 snRNA


Mass: 182114.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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U1 small nuclear ribonucleoprotein ... , 5 types, 5 molecules QRSTX

#3: Protein U1 small nuclear ribonucleoprotein 70 kDa homolog / U1-70K / U1 small nuclear ribonucleoprotein SNP1 / U1 snRNP protein SNP1


Mass: 34506.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q00916
#4: Protein U1 small nuclear ribonucleoprotein C / U1C


Mass: 27106.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q05900
#5: Protein U1 small nuclear ribonucleoprotein A / U1A / Mutant U1 die protein 1


Mass: 34438.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P32605
#6: Protein U1 small nuclear ribonucleoprotein component PRP42 / U1 snRNP protein PRP42 / 65 kDa snRNP protein / Pre-mRNA-processing factor 42


Mass: 65222.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q03776
#17: Protein U1 small nuclear ribonucleoprotein component SNU71


Mass: 71383.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P53207

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Protein , 6 types, 6 molecules UVWaYy

#7: Protein Pre-mRNA-processing factor 39


Mass: 74834.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P39682
#8: Protein Protein NAM8


Mass: 57010.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q00539
#9: Protein 56 kDa U1 small nuclear ribonucleoprotein component


Mass: 56575.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q03782
#10: 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 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P40018
#18: Protein Protein LUC7


Mass: 30245.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q07508
#20: Protein Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 / Helicase CA8 / Coordinate model: Cα atoms only


Mass: 66733.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P23394, RNA helicase

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

#11: 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 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q02260
#12: 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 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q06217
#13: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 11240.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P43321
#14: 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 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: Q12330
#15: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9669.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P54999
#16: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8490.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P40204

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Protein/peptide / Non-polymers , 2 types, 4 molecules x

#19: Protein/peptide U1 snRNP


Mass: 3500.827 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#21: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsRegarding the U1 snRNP (chain x), due to the relative low resolution, authors can not confirm the ...Regarding the U1 snRNP (chain x), due to the relative low resolution, authors can not confirm the sequence and identity.

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Pre-B spliceosomal complex / Type: CELL / Entity ID: #1-#20 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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 FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM softwareName: RELION / Version: 2 / Category: 3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 500657 / Algorithm: FOURIER SPACE / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Refinement stepCycle: 1 / Total: 33541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0150.01635242
ELECTRON MICROSCOPYr_bond_other_d0.0040.0226435
ELECTRON MICROSCOPYr_angle_refined_deg1.7621.70450264
ELECTRON MICROSCOPYr_angle_other_deg1.368361161
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.40152956
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.65224.195901
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.103153666
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.52115112
ELECTRON MICROSCOPYr_chiral_restr0.1130.25718
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0232112
ELECTRON MICROSCOPYr_gen_planes_other0.0040.027790
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_it10.37310.14711917
ELECTRON MICROSCOPYr_mcbond_other10.36610.14611916
ELECTRON MICROSCOPYr_mcangle_it17.24915.20814842
ELECTRON MICROSCOPYr_mcangle_other17.2515.20914843
ELECTRON MICROSCOPYr_scbond_it10.7916.80523325
ELECTRON MICROSCOPYr_scbond_other10.7916.80523326
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other17.88625.35135423
ELECTRON MICROSCOPYr_long_range_B_refined29.387146469
ELECTRON MICROSCOPYr_long_range_B_other29.387146470
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.477 38897 -
Rfree-0 -
obs--100 %

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