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- PDB-6id0: Cryo-EM structure of a human intron lariat spliceosome prior to P... -

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Basic information

Entry
Database: PDB / ID: 6id0
TitleCryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 complex) at 2.9 angstrom resolution
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 4
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • CWF19-like protein 2
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • RNA helicase aquarius
  • SNW domain-containing protein 1
  • Small nuclear ribonucleoprotein-associated protein
  • Spliceosome-associated protein CWC15 homolog
  • U2snRNA
  • U5 small nuclear ribonucleoprotein 40 kDa protein
  • U5snRNA
  • U6snRNA
  • pre-mRNAPrimary transcript
KeywordsSPLICING / Human Intron Lariat Spliceosome
Function / homology
Function and homology information


snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / post-mRNA release spliceosomal complex / U7 snRNP / 7-methylguanosine cap hypermethylation / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / histone pre-mRNA 3'end processing complex ...snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / post-mRNA release spliceosomal complex / U7 snRNP / 7-methylguanosine cap hypermethylation / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / histone pre-mRNA 3'end processing complex / generation of catalytic spliceosome for first transesterification step / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of vitamin D receptor signaling pathway / U2-type prespliceosome assembly / methylosome / protein methylation / U12-type spliceosomal complex / embryonic brain development / pre-mRNA binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / nuclear retinoic acid receptor binding / RNA splicing, via transesterification reactions / Prp19 complex / 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 / U2-type catalytic step 2 spliceosome / U2 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 / Notch binding / nuclear vitamin D receptor binding / RNA Polymerase II Transcription Termination / U1 snRNP / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / ubiquitin-ubiquitin ligase activity / spliceosomal complex assembly / U2-type prespliceosome / RUNX3 regulates NOTCH signaling / K63-linked polyubiquitin modification-dependent protein binding / NOTCH4 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / positive regulation of neurogenesis / lipid biosynthetic process / NOTCH3 Intracellular Domain Regulates Transcription / precatalytic spliceosome / nuclear androgen receptor binding / cyclosporin A binding / mRNA Splicing - Minor Pathway / Notch-HLH transcription pathway / Formation of paraxial mesoderm / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / protein K63-linked ubiquitination / mitotic G2 DNA damage checkpoint signaling / 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 / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNP / retinoic acid receptor signaling pathway / spliceosomal snRNP assembly / positive regulation of viral genome replication / embryonic organ development / Cajal body / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / protein peptidyl-prolyl isomerization / U1 snRNA binding / gastrulation / cellular response to retinoic acid / 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
Similarity search - Function
Cwf19-like protein, C-terminal domain-2 / Cwf19-like, C-terminal domain-1 / Cwf19-like protein / Protein similar to CwfJ C-terminus 2 / Protein similar to CwfJ C-terminus 1 / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Pre-mRNA-splicing factor SPF27 ...Cwf19-like protein, C-terminal domain-2 / Cwf19-like, C-terminal domain-1 / Cwf19-like protein / Protein similar to CwfJ C-terminus 2 / Protein similar to CwfJ C-terminus 1 / : / : / 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 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Pre-mRNA-processing factor 17 / DNA2/NAM7-like helicase / : / 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 / Small ribonucleoprotein associated, SmB/SmN / 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 / 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 / Small nuclear ribonucleoprotein D1 / U2 small nuclear ribonucleoprotein A' / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / U-box domain profile. / Pre-mRNA-splicing factor Syf1-like / Leucine-rich repeat / Modified RING finger domain / Snu114, GTP-binding domain / U-box domain / 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 / Zinc finger, CCCH-type superfamily / zinc finger / HIT-like superfamily / Small nuclear ribonucleoprotein Sm D3 / 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 / Sm-like protein Lsm6/SmF / SH3 type barrels. - #100 / Myb-type HTH DNA-binding domain profile. / Zinc finger, CCCH-type / LSM domain / Zinc finger C3H1-type profile. / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Myb domain / : / Sm domain profile. / Cyclophilin-like / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin / Elongation Factor G, domain II / Elongation Factor G, domain III / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Tetratricopeptide repeat / Translation elongation factor EFG/EF2, domain IV / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Elongation factor G, domain IV / Elongation factor G, domain IV / LSM domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Pleiotropic regulator 1 / RNA helicase aquarius / Pre-mRNA-processing factor 17 ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Pleiotropic regulator 1 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / 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' / 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 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / CWF19-like protein 2 / Small nuclear ribonucleoprotein-associated protein / Pre-mRNA-processing-splicing factor 8 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Crooked neck-like protein 1 / 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 / Peptidyl-prolyl cis-trans isomerase-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang, X. / Zhan, X. / Yan, C. / Shi, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China31430020 China
CitationJournal: Cell Res / Year: 2019
Title: Structures of the human spliceosomes before and after release of the ligated exon.
Authors: Xiaofeng Zhang / Xiechao Zhan / Chuangye Yan / Wenyu Zhang / Dongliang Liu / Jianlin Lei / Yigong Shi /
Abstract: Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ...Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this study, we report the cryo-electron microscopy structures of the human post-catalytic spliceosome (P complex) and intron lariat spliceosome (ILS) at average resolutions of 3.0 and 2.9 Å, respectively. In the P complex, the ligated exon remains anchored to loop I of U5 small nuclear RNA, and the 3'-splice site is recognized by the junction between the 5'-splice site and the branch point sequence. The ATPase/helicase Prp22, along with the ligated exon and eight other proteins, are dissociated in the P-to-ILS transition. Intriguingly, the ILS complex exists in two distinct conformations, one with the ATPase/helicase Prp43 and one without. Comparison of these three late-stage human spliceosomes reveals mechanistic insights into exon release and spliceosome disassembly.
History
DepositionSep 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Oct 14, 2020Group: Atomic model / Data collection ...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 / struct_conn / struct_conn_type / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: U5snRNA
C: 116 kDa U5 small nuclear ribonucleoprotein component
E: U5 small nuclear ribonucleoprotein 40 kDa protein
F: U6snRNA
J: Crooked neck-like protein 1
L: Cell division cycle 5-like protein
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
W: Pre-mRNA-processing factor 17
G: pre-mRNA
H: U2snRNA
U: CWF19-like protein 2
I: Pre-mRNA-splicing factor SYF1
a: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated protein
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
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
h: Small nuclear ribonucleoprotein Sm D3
i: Small nuclear ribonucleoprotein-associated protein
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''
Q: RNA helicase aquarius
y: Peptidyl-prolyl cis-trans isomerase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,056,45158
Polymers2,054,64042
Non-polymers1,81116
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 12 types, 13 molecules ACEJLNPRTUbiQ

#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
#4: 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
#6: 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
#7: 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
#9: 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
#11: 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
#12: 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
#14: 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
#18: Protein CWF19-like protein 2


Mass: 103976.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q2TBE0
#21: Protein Small nuclear ribonucleoprotein-associated protein


Mass: 23686.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q66K91, UniProt: P14678*PLUS
#31: Protein RNA helicase 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, RNA helicase

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RNA chain , 4 types, 4 molecules BFGH

#2: RNA chain U5snRNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981
#5: RNA chain U6snRNA


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


Mass: 87186.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#17: RNA chain U2snRNA


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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Pre-mRNA-splicing factor ... , 4 types, 4 molecules MOIK

#8: 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
#10: 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
#19: 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
#28: 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

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Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Sy

#13: 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
#32: 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

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

#15: 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
#27: 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 ahcjdkfmelgn

#20: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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

#29: 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
#30: 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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Non-polymers , 4 types, 16 molecules

#33: 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
#34: 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
#35: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#36: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / 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 Intron Lariat Spliceosome / Type: COMPLEX / Entity ID: #1-#32 / 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
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 390072 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å

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