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- PDB-5yzg: The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C co... -

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Basic information

Entry
Database: PDB / ID: 5yzg
TitleThe Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution
Components
  • (Peptidyl-prolyl cis-trans isomerase ...Prolyl isomerase) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 8
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Cell division cycle 5-like protein
  • Coiled-coil domain-containing protein 94
  • Crooked neck-like protein 1
  • Eukaryotic initiation factor 4A-III
  • Intron-binding protein aquarius
  • Peptidyl-prolyl cis-trans isomerase-like 1
  • Peptidylprolyl isomerase domain and WD repeat-containing protein 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Pre-mRNAPrimary transcript
  • Protein BUD31 homolog
  • Protein CASC3
  • Protein mago nashi homolog 2
  • RNA-binding protein 8A
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 2
  • 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
  • UNKNOW
KeywordsSPLICING / Structure of a Human Catalytic Step I Spliceosome
Function / homology
Function and homology information


exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex ...exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / intracellular mRNA localization / histone pre-mRNA DCP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNP / 3'-5' RNA helicase activity / regulation of translation at postsynapse, modulating synaptic transmission / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / negative regulation of excitatory postsynaptic potential / regulation of vitamin D receptor signaling pathway / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / Deadenylation of mRNA / embryonic brain development / methylosome / protein methylation / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / pre-mRNA binding / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / Prp19 complex / poly(A) binding / positive regulation of androgen receptor activity / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / M-decay: degradation of maternal mRNAs by maternally stored factors / P granule / RNA stem-loop binding / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / embryonic cranial skeleton morphogenesis / telomerase RNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / positive regulation by host of viral transcription / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / U2 snRNP / Notch binding / nuclear vitamin D receptor binding / RNA Polymerase II Transcription Termination / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U1 snRNP / RUNX3 regulates NOTCH signaling / U2-type prespliceosome / NOTCH4 Intracellular Domain Regulates Transcription / K63-linked polyubiquitin modification-dependent protein binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ubiquitin-ubiquitin ligase activity / exploration behavior / lipid biosynthetic process / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / nuclear androgen receptor binding / cyclosporin A binding / spliceosomal complex assembly / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / Formation of paraxial mesoderm / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / protein K63-linked ubiquitination / mitotic G2 DNA damage checkpoint signaling / negative regulation of DNA damage response, signal transduction by p53 class mediator / mRNA 3'-splice site recognition / associative learning / blastocyst development
Similarity search - Function
CBF1-interacting co-repressor CIR, N-terminal domain / Pre-mRNA splicing factor / N-terminal domain of CBF1 interacting co-repressor CIR / Pre-mRNA splicing factor / N-terminal domain of CBF1 interacting co-repressor CIR / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / Saf4/Yju2 protein / Splicing factor Yju2 ...CBF1-interacting co-repressor CIR, N-terminal domain / Pre-mRNA splicing factor / N-terminal domain of CBF1 interacting co-repressor CIR / Pre-mRNA splicing factor / N-terminal domain of CBF1 interacting co-repressor CIR / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / Saf4/Yju2 protein / Splicing factor Yju2 / Saf4/Yju2 protein / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / : / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / mRNA splicing factor SYF2 / SYF2 splicing factor / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / U2 small nuclear ribonucleoprotein A' / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Helix hairpin bin domain superfamily / mRNA splicing factor Cwf21 domain / cwf21 domain / Pre-mRNA-processing factor 17 / : / STL11, N-terminal / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / : / U-box domain / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / WD repeat Prp46/PLRG1-like / BUD31/G10-related, conserved site / : / : / G10 protein signature 1. / G10 protein signature 2. / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Myb-like DNA-binding domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / HAT (Half-A-TPR) repeat / Cwf15/Cwc15 cell cycle control protein / Small ribonucleoprotein associated, SmB/SmN / Pre-mRNA-splicing factor Cwc2/Slt11 / G10 protein / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / pre-mRNA splicing factor component / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / Small nuclear ribonucleoprotein D1 / MIF4G domain / Spt5 C-terminal 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. / Leucine-rich repeat / Modified RING finger domain / Pre-mRNA-splicing factor Syf1-like / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / U-box domain / Snu114, GTP-binding domain / Sec63 Brl domain / Zinc finger, CCCH-type superfamily / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / : / Helicase associated domain (HA2), ratchet-like / zinc finger
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / Protein CASC3 / Pleiotropic regulator 1 / RNA helicase aquarius ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / Protein CASC3 / Pleiotropic regulator 1 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / Pre-mRNA-splicing factor SYF2 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein-associated proteins B and B' / Eukaryotic initiation factor 4A-III / 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 / Peptidyl-prolyl cis-trans isomerase G / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Pre-mRNA-processing-splicing factor 8 / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / Protein mago nashi homolog 2 / Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Splicing factor YJU2 / Crooked neck-like protein 1 / Pre-mRNA-splicing factor CWC22 homolog / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / Pre-mRNA-splicing factor CWC25 homolog / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase E / Serine/arginine repetitive matrix protein 2 / Peptidyl-prolyl cis-trans isomerase-like 1 / RNA-binding protein 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZhan, X. / Yan, C. / Zhang, X. / Lei, J. / Shi, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2014ZX09507003006 China
National Natural Science Foundation of China31130002 China
National Natural Science Foundation of China31321062 China
CitationJournal: Science / Year: 2018
Title: Structure of a human catalytic step I spliceosome.
Authors: Xiechao Zhan / Chuangye Yan / Xiaofeng Zhang / Jianlin Lei / Yigong Shi /
Abstract: Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron ...Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron microscopy structure of the human C complex at an average resolution of 4.1 angstroms. Compared with the C complex, the human complex contains 11 additional proteins. The step I splicing factors CCDC49 and CCDC94 (Cwc25 and Yju2 in , respectively) closely interact with the DEAH-family adenosine triphosphatase/helicase Prp16 and bridge the gap between Prp16 and the active-site RNA elements. These features, together with structural comparison of the human C and C* complexes, provide mechanistic insights into ribonucleoprotein remodeling and allow the proposition of a working mechanism for the C-to-C* transition.
History
DepositionDec 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 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 2.0Oct 14, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / 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 / _entity_poly.pdbx_seq_one_letter_code / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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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
F: U6 snRNA
G: Pre-mRNA
H: U2 snRNA
I: Pre-mRNA-splicing factor SYF1
J: Crooked neck-like protein 1
K: Pre-mRNA-splicing factor SPF27
L: Cell division cycle 5-like protein
y: Pre-mRNA-splicing factor ISY1 homolog
M: Pre-mRNA-splicing factor SYF2
N: Protein BUD31 homolog
O: Pre-mRNA-splicing factor RBM22
P: Spliceosome-associated protein CWC15 homolog
R: SNW domain-containing protein 1
S: Peptidyl-prolyl cis-trans isomerase-like 1
T: Pleiotropic regulator 1
Q: Intron-binding protein aquarius
U: Serine/arginine repetitive matrix protein 2
V: Pre-mRNA-splicing factor CWC22 homolog
W: Pre-mRNA-processing factor 17
X: Pre-mRNA-splicing factor CWC25 homolog
Y: Coiled-coil domain-containing protein 94
Z: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
u: Eukaryotic initiation factor 4A-III
v: Protein mago nashi homolog 2
w: RNA-binding protein 8A
x: Protein CASC3
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''
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
1: Peptidyl-prolyl cis-trans isomerase E
2: Peptidylprolyl isomerase domain and WD repeat-containing protein 1
3: Peptidyl-prolyl cis-trans isomerase G
4: UNKNOW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,193,81574
Polymers3,190,64355
Non-polymers3,17319
Water0
1


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

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Components

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Protein , 18 types, 19 molecules ACJLNPRSTQUYuvwxib2

#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
#10: 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
#12: 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
#15: 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
#17: 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
#18: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61770.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#19: 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
#20: 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
#21: 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
#22: 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
#26: Protein Coiled-coil domain-containing protein 94


Mass: 37141.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW85
#29: Protein Eukaryotic initiation factor 4A-III / eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box ...eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Eukaryotic translation initiation factor 4A isoform 3 / Nuclear matrix protein 265 / hNMP 265


Mass: 46930.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P38919, RNA helicase
#30: Protein Protein mago nashi homolog 2


Mass: 17301.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A72
#31: Protein RNA-binding protein 8A / Binder of OVCA1-1 / BOV-1 / RNA-binding motif protein 8A / RNA-binding protein Y14 / Ribonucleoprotein RBM8A


Mass: 19925.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5S9
#32: Protein Protein CASC3 / Cancer susceptibility candidate gene 3 protein / Metastatic lymph node gene 51 protein / MLN 51 / ...Cancer susceptibility candidate gene 3 protein / Metastatic lymph node gene 51 protein / MLN 51 / Protein barentsz / Btz


Mass: 76381.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15234
#34: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 23459.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#43: Protein Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / Spliceosome-associated cyclophilin


Mass: 73679.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP3, peptidylprolyl isomerase

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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)
#6: 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)
#7: RNA chain Pre-mRNA / Primary transcript


Mass: 88088.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#8: 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)

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

#4: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 ...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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Pre-mRNA-splicing factor ... , 8 types, 8 molecules IKyMOVXZ

#9: 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
#11: 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
#13: Protein Pre-mRNA-splicing factor ISY1 homolog


Mass: 35499.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULR0
#14: Protein Pre-mRNA-splicing factor SYF2 / CCNDBP1-interactor / p29


Mass: 28780.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95926
#16: 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
#23: 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
#25: Protein Pre-mRNA-splicing factor CWC25 homolog / Coiled-coil domain-containing protein 49 / Spliceosome-associated protein homolog CWC25


Mass: 49736.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NXE8
#27: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / ATP-dependent RNA helicase DHX38 / DEAH box protein 38


Mass: 140720.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92620, RNA helicase

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Pre-mRNA-processing factor ... , 2 types, 5 molecules Wqrst

#24: 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
#28: 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

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

#33: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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

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

#40: 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
#41: 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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Peptidyl-prolyl cis-trans isomerase ... , 2 types, 2 molecules 13

#42: 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
#44: Protein Peptidyl-prolyl cis-trans isomerase G / Peptidyl-prolyl isomerase G / CASP10 / Clk-associating RS-cyclophilin / SRcyp / Cyclophilin G / Rotamase G


Mass: 88854.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13427, peptidylprolyl isomerase

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Protein/peptide , 1 types, 1 molecules 4

#45: Protein/peptide UNKNOW


Mass: 2631.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 6 types, 19 molecules

#46: 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
#47: 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
#48: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#49: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#50: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#51: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

+
Details

Sequence detailsThe N (unknown nucleotide) between G-1 and G1 is added intentionally to fill in the cleavage by RNA splicing.

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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 Catalytic Step I Spliceosome / Type: COMPLEX / Entity ID: #1-#45 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
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: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
EM software
IDNameVersionCategory
4Gctf0.66CTF correction
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1464033
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53633 / Algorithm: FOURIER SPACE / Symmetry type: POINT
RefinementHighest resolution: 4.1 Å
Refinement stepCycle: 1 / Total: 55623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0160.01857399
ELECTRON MICROSCOPYr_bond_other_d0.0030.0250656
ELECTRON MICROSCOPYr_angle_refined_deg1.8831.8779000
ELECTRON MICROSCOPYr_angle_other_deg1.0423116696
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.60156170
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.31623.552341
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.471158765
ELECTRON MICROSCOPYr_dihedral_angle_4_deg21.0415382
ELECTRON MICROSCOPYr_chiral_restr0.0980.28624
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.02160078
ELECTRON MICROSCOPYr_gen_planes_other0.0030.0213269
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_it15.03615.56924872
ELECTRON MICROSCOPYr_mcbond_other15.03515.56924871
ELECTRON MICROSCOPYr_mcangle_it24.8923.26430978
ELECTRON MICROSCOPYr_mcangle_other24.8923.26430979
ELECTRON MICROSCOPYr_scbond_it17.71717.27632527
ELECTRON MICROSCOPYr_scbond_other17.71717.27732528
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other30.19725.38148023
ELECTRON MICROSCOPYr_long_range_B_refined47.913240216
ELECTRON MICROSCOPYr_long_range_B_other47.913240217
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.1→4.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.542 31339 -
Rfree-0 -
obs--100 %

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