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- PDB-5z56: cryo-EM structure of a human activated spliceosome (mature Bact) ... -

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Basic information

Entry
Database: PDB / ID: 5z56
Titlecryo-EM structure of a human activated spliceosome (mature Bact) at 5.1 angstrom.
Components
  • (Peptidyl-prolyl cis-trans isomerase ...Prolyl isomerase) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 4
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (Splicing factor 3A subunit ...) x 3
  • (Splicing factor 3B subunit ...) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • BUD13 homolog
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • Intron-binding protein aquarius
  • PHD finger-like domain-containing protein 5A
  • Peptidyl-prolyl cis-trans isomerase-like 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
  • RING finger protein 113A
  • RNA-binding motif protein, X-linked 2
  • Serine/arginine repetitive matrix protein 2
  • Skip
  • Smad nuclear-interacting protein 1
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • U2 snRNAU2 spliceosomal RNA
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
  • pre-mRNAPrimary transcript
KeywordsSPLICING / human activated spliceosome / mature Bact / pre-mRNA splicing
Function / homology
Function and homology information


RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / post-mRNA release spliceosomal complex / U7 snRNP ...RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / post-mRNA release spliceosomal complex / U7 snRNP / 7-methylguanosine cap hypermethylation / 3'-5' RNA helicase activity / B-WICH complex / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / U2-type prespliceosome assembly / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / methylosome / protein methylation / splicing factor binding / U12-type spliceosomal complex / embryonic brain development / miRNA processing / pre-mRNA binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / Prp19 complex / blastocyst formation / U4 snRNP / spliceosomal tri-snRNP complex / poly(A) binding / small nuclear ribonucleoprotein complex / P granule / positive regulation of androgen receptor activity / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA 3'-end processing / U2-type spliceosomal complex / : / telomerase RNA binding / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / commitment complex / regulation of mRNA splicing, via spliceosome / U2-type catalytic step 2 spliceosome / C2H2 zinc finger domain binding / U2 snRNP / Transport of Mature mRNA derived from an Intron-Containing Transcript / SAGA complex / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / spliceosomal complex assembly / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / pattern recognition receptor activity / WD40-repeat domain binding / lipid biosynthetic process / precatalytic spliceosome / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / protein K63-linked ubiquitination / antiviral innate immune response / mRNA 3'-splice site recognition / blastocyst development / RNA processing / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / transcription-coupled nucleotide-excision repair / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / spliceosomal snRNP assembly / positive regulation of viral genome replication / regulation of DNA repair / Cajal body / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / protein peptidyl-prolyl isomerization / U1 snRNA binding / translation elongation factor activity / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / catalytic step 2 spliceosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA Splicing - Major Pathway / lipid droplet / positive regulation of RNA splicing / RNA splicing
Similarity search - Function
Pre-mRNA-splicing factor CWC24-like / Ist3-like, RNA recognition motif / Bud13 / Pre-mRNA-splicing factor of RES complex / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / SF3B6, RNA recognition motif / : ...Pre-mRNA-splicing factor CWC24-like / Ist3-like, RNA recognition motif / Bud13 / Pre-mRNA-splicing factor of RES complex / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / SF3B6, RNA recognition motif / : / Pre-mRNA-splicing factor SPF27 / Splicing factor 3A subunit 1, ubiquitin domain / Breast carcinoma amplified sequence 2 (BCAS2) / SF3B4, RNA recognition motif 2 / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / Peptidyl-prolyl cis-trans isomerase E / Splicing factor SF3a60 binding domain / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Splicing factor SF3a60 binding domain / : / Replication stress response SDE2 C-terminal / Cactus-binding C-terminus of cactin protein / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / SF3A2 domain / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3B4, RNA recognition motif 1 / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Splicing factor 3B, subunit 5 / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / mRNA splicing factor Cwf21 domain / cwf21 domain / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Domain of unknown function DUF382 / Pre-mRNA-processing factor 17 / DNA2/NAM7-like helicase / Domain of unknown function (DUF382) / : / STL11, N-terminal / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / : / U-box domain / DNA2/NAM7 helicase, helicase domain / AAA domain / WD repeat Prp46/PLRG1-like / Zinc-finger of C2H2 type / Small ribonucleoprotein associated, SmB/SmN / BUD31/G10-related, conserved site / : / : / G10 protein signature 1. / G10 protein signature 2. / PHF5-like / PHF5-like protein / PSP, proline-rich / PSP / Myb-like DNA-binding domain / proline-rich domain in spliceosome associated proteins / Pre-mRNA-splicing factor Cwf15/Cwc15 / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / HAT (Half-A-TPR) repeat / Cwf15/Cwc15 cell cycle control protein / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Pre-mRNA-splicing factor Cwc2/Slt11 / Matrin/U1-C, C2H2-type zinc finger / Splicing factor 3B subunit 1-like / Zinc finger matrin-type profile. / G10 protein / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / pre-mRNA splicing factor component / Small nuclear ribonucleoprotein D1 / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / U2 small nuclear ribonucleoprotein A' / Spt5 C-terminal domain / MIF4G domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / U-box domain profile.
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein-associated proteins B and B' / Protein BUD31 homolog / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / Splicing factor 3B subunit 4 / Splicing factor 3A subunit 2 / Splicing factor 3A subunit 1 / Pre-mRNA-processing-splicing factor 8 / Spliceosome-associated protein CWC27 homolog / PHD finger-like domain-containing protein 5A / Smad nuclear-interacting protein 1 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / BUD13 homolog / Splicing factor 3B subunit 5 / Crooked neck-like protein 1 / Pre-mRNA-splicing factor CWC22 homolog / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase E / Serine/arginine repetitive matrix protein 2 / RNA-binding motif protein, X-linked 2 / Splicing factor 3B subunit 6 / Peptidyl-prolyl cis-trans isomerase-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified adenovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsZhang, X. / Yan, C. / Zhan, X. / Li, L. / Lei, J. / Shi, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China31430020 China
Ministry of Science and Technology (China)2016YFA0501100 China
CitationJournal: Cell Res / Year: 2018
Title: Structure of the human activated spliceosome in three conformational states.
Authors: Xiaofeng Zhang / Chuangye Yan / Xiechao Zhan / Lijia Li / Jianlin Lei / Yigong Shi /
Abstract: During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to ...During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we present the cryo-EM structure of the human B complex in three distinct conformational states. The EM map allows atomic modeling of nearly all protein components of the U2 small nuclear ribonucleoprotein (snRNP), including three of the SF3a complex and seven of the SF3b complex. The structure of the human B complex contains 52 proteins, U2, U5, and U6 small nuclear RNA (snRNA), and a pre-mRNA. Three distinct conformations have been captured, representing the early, mature, and late states of the human B complex. These complexes differ in the orientation of the Switch loop of Prp8, the splicing factors RNF113A and NY-CO-10, and most components of the NineTeen complex (NTC) and the NTC-related complex. Analysis of these three complexes and comparison with the B and C complexes reveal an ordered flux of components in the B-to-B and the B-to-B transitions, which ultimately prime the active site for the branching reaction.
History
DepositionJan 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: pdbx_database_related
Item: _pdbx_database_related.content_type / _pdbx_database_related.details
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 2.0Oct 14, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: U5 snRNA
C: 116 kDa U5 small nuclear ribonucleoprotein component
D: U5 small nuclear ribonucleoprotein 200 kDa helicase
E: U5 small nuclear ribonucleoprotein 40 kDa protein
a: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated proteins B and B'
c: Small nuclear ribonucleoprotein Sm D1
d: Small nuclear ribonucleoprotein Sm D2
f: Small nuclear ribonucleoprotein F
e: Small nuclear ribonucleoprotein E
g: Small nuclear ribonucleoprotein G
F: U6 snRNA
G: pre-mRNA
H: U2 snRNA
h: Small nuclear ribonucleoprotein Sm D3
i: Small nuclear ribonucleoprotein-associated proteins B and B'
j: Small nuclear ribonucleoprotein Sm D1
k: Small nuclear ribonucleoprotein Sm D2
m: Small nuclear ribonucleoprotein F
l: Small nuclear ribonucleoprotein E
n: Small nuclear ribonucleoprotein G
o: U2 small nuclear ribonucleoprotein A'
p: U2 small nuclear ribonucleoprotein B''
w: Splicing factor 3A subunit 3
u: Splicing factor 3A subunit 1
v: Splicing factor 3A subunit 2
1: Splicing factor 3B subunit 1
2: Splicing factor 3B subunit 2
3: Splicing factor 3B subunit 3
4: Splicing factor 3B subunit 4
5: Splicing factor 3B subunit 6
6: PHD finger-like domain-containing protein 5A
7: Splicing factor 3B subunit 5
J: Crooked neck-like protein 1
L: Cell division cycle 5-like protein
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
K: Pre-mRNA-splicing factor SPF27
I: Pre-mRNA-splicing factor SYF1
Q: Intron-binding protein aquarius
M: RING finger protein 113A
N: Protein BUD31 homolog
O: Pre-mRNA-splicing factor RBM22
P: Spliceosome-associated protein CWC15 homolog
R: Skip
S: Peptidyl-prolyl cis-trans isomerase-like 1
T: Pleiotropic regulator 1
U: Serine/arginine repetitive matrix protein 2
V: Pre-mRNA-splicing factor CWC22 homolog
W: Pre-mRNA-processing factor 17
X: Smad nuclear-interacting protein 1
Y: RNA-binding motif protein, X-linked 2
Z: BUD13 homolog
z: Peptidyl-prolyl cis-trans isomerase CWC27 homolog
x: Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
y: Peptidyl-prolyl cis-trans isomerase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,602,98980
Polymers3,600,81059
Non-polymers2,17921
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 18 types, 19 molecules ACbi6JLQMNPRSTUXYZx

#1: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#3: Protein 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP- ...Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#7: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 23686.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#26: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b


Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0
#28: Protein Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#29: Protein Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#33: Protein Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 171502.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60306
#34: Protein RING finger protein 113A / / Zinc finger protein 183


Mass: 38847.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15541
#35: Protein Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#37: Protein Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#38: Protein Skip


Mass: 62063.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#39: Protein Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#40: Protein Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#41: Protein Serine/arginine repetitive matrix protein 2 / 300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix ...300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related nuclear matrix protein of 300 kDa / Splicing coactivator subunit SRm300 / Tax-responsive enhancer element-binding protein 803 / TaxREB803


Mass: 300255.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35
#44: Protein Smad nuclear-interacting protein 1 / FHA domain-containing protein SNIP1


Mass: 45880.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAD8
#45: Protein RNA-binding motif protein, X-linked 2


Mass: 37425.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y388
#46: Protein BUD13 homolog


Mass: 70669.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRD0
#48: Protein Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / ATP-dependent RNA helicase #3 / DEAH-box protein 16


Mass: 119443.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60231, RNA helicase

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RNA chain , 4 types, 4 molecules BFGH

#2: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981
#13: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 34404.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#14: RNA chain pre-mRNA / Primary transcript


Mass: 87892.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus
#15: RNA chain U2 snRNA / U2 spliceosomal RNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 340097

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U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules DE

#4: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Brr2 / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific ...Brr2 / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#5: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein ...U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57


Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7

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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahcjdkfmelgn

#6: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#8: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#9: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#10: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#11: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#12: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

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U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op

#16: Protein U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 28456.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09661
#17: Protein U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08579

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Splicing factor 3A subunit ... , 3 types, 3 molecules wuv

#18: Protein Splicing factor 3A subunit 3 / SF3a60 / Spliceosome-associated protein 61 / SAP 61


Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12874
#19: Protein Splicing factor 3A subunit 1 / SF3a120 / Spliceosome-associated protein 114 / SAP 114


Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459
#20: Protein Splicing factor 3A subunit 2 / SF3a66 / Spliceosome-associated protein 62 / SAP 62


Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15428

+
Splicing factor 3B subunit ... , 6 types, 6 molecules 123457

#21: Protein Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155


Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533
#22: Protein Splicing factor 3B subunit 2 / Pre-mRNA-splicing factor SF3b 145 kDa subunit / SF3b145 / Spliceosome-associated protein 145 / SAP 145


Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435
#23: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393
#24: Protein Splicing factor 3B subunit 4 / Pre-mRNA-splicing factor SF3b 49 kDa subunit / Spliceosome-associated protein 49 / SAP 49


Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15427
#25: Protein Splicing factor 3B subunit 6 / Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / ...Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / 14-kDa / Splicing factor 3b / subunit 6 / 14kDa


Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B4
#27: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5

+
Pre-mRNA-processing factor ... , 2 types, 5 molecules qrstW

#30: Protein
Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 ...Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 / Senescence evasion factor


Mass: 55245.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase
#43: Protein Pre-mRNA-processing factor 17 / Cell division cycle 40 homolog / EH-binding protein 3 / Ehb3 / PRP17 homolog / hPRP17


Mass: 65612.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60508

+
Pre-mRNA-splicing factor ... , 4 types, 4 molecules KIOV

#31: Protein Pre-mRNA-splicing factor SPF27 / Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome- ...Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome-associated protein SPF 27


Mass: 26163.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75934
#32: Protein Pre-mRNA-splicing factor SYF1 / Protein HCNP / XPA-binding protein 2


Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#36: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#42: Protein Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb


Mass: 105646.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8

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Peptidyl-prolyl cis-trans isomerase ... , 2 types, 2 molecules zy

#47: Protein Peptidyl-prolyl cis-trans isomerase CWC27 homolog / PPIase CWC27 / Antigen NY-CO-10 / Serologically defined colon cancer antigen 10


Mass: 53941.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6UX04, peptidylprolyl isomerase
#49: Protein Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E


Mass: 33475.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNP9, peptidylprolyl isomerase

+
Non-polymers , 4 types, 21 molecules

#50: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#51: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#52: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#53: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn

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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: human activated spliceosome / Type: COMPLEX / Entity ID: #1-#49 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9 / Details: 20 mM HEPES-KOH, 150 mM NaCl, 1.5 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELDBright-field microscopy / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2DigitalMicrograph2image acquisition
4Gctf0.66CTF correction
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27405 / Algorithm: FOURIER SPACE / Symmetry type: POINT
RefinementHighest resolution: 5.1 Å

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