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

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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


positive regulation of vitamin D receptor signaling pathway / cellular response to wortmannin / cellular response to interleukin-2 / cellular response to prolactin / U2 snRNP binding / snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / leucine zipper domain binding / U7 snRNP ...positive regulation of vitamin D receptor signaling pathway / cellular response to wortmannin / cellular response to interleukin-2 / cellular response to prolactin / U2 snRNP binding / snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / leucine zipper domain binding / U7 snRNP / signal transduction involved in DNA damage checkpoint / histone pre-mRNA 3'end processing complex / methylosome / histone mRNA metabolic process / regulation of vitamin D receptor signaling pathway / telomerase holoenzyme complex / RNA splicing, via transesterification reactions / inner cell mass cell proliferation / mitotic G2 DNA damage checkpoint / generation of catalytic spliceosome for first transesterification step / positive regulation of androgen receptor activity / positive regulation of neurogenesis / hair cycle / U1 snRNP binding / positive regulation of astrocyte differentiation / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / protein phosphatase 1 binding / transcription corepressor binding / WD40-repeat domain binding / telomerase RNA binding / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / ubiquitin-ubiquitin ligase activity / U4 snRNP / small nuclear ribonucleoprotein complex / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / spliceosomal tri-snRNP complex / retinoic acid receptor binding / U5 snRNA binding / poly(A) binding / SMN-Sm protein complex / import into nucleus / U2 snRNA binding / pre-mRNA binding / mRNA cis splicing, via spliceosome / protein methylation / positive regulation by host of viral transcription / U2-type catalytic step 2 spliceosome / commitment complex / spliceosomal tri-snRNP complex assembly / U12-type spliceosomal complex / U2 snRNP / Prp19 complex / vitamin D receptor binding / U6 snRNA binding / Notch binding / K63-linked polyubiquitin modification-dependent protein binding / Cul4-RING E3 ubiquitin ligase complex / small nucleolar ribonucleoprotein complex / blastocyst development / U5 snRNP / spliceosomal complex assembly / precatalytic spliceosome / mRNA 3'-end processing / U2-type prespliceosome / spliceosomal snRNP assembly / P granule / U1 snRNP / U4/U6 x U5 tri-snRNP complex / positive regulation of transcription of Notch receptor target / U1 snRNA binding / pre-mRNA intronic binding / lipid biosynthetic process / protein K63-linked ubiquitination / cellular response to fibroblast growth factor stimulus / cyclosporin A binding / RNA export from nucleus / positive regulation of histone H3-K4 methylation / protein localization to nucleus / retinoic acid receptor signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / RNA processing / gastrulation / lipid droplet / positive regulation of Notch signaling pathway / termination of RNA polymerase II transcription / catalytic step 2 spliceosome / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of viral genome replication / SMAD binding / embryonic organ development / positive regulation of G1/S transition of mitotic cell cycle / cellular protein localization / response to cocaine / Cajal body / protein peptidyl-prolyl isomerization / mRNA export from nucleus / cellular response to nerve growth factor stimulus
Zinc finger, RING/FYVE/PHD-type / G-protein beta WD-40 repeat / Small nuclear ribonucleoprotein E / CWF11 family / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / PRP8 domain IV core / Pre-mRNA splicing factor component Cdc5p/Cef1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Ribosomal protein S5 domain 2-type fold / WD40 repeat, conserved site ...Zinc finger, RING/FYVE/PHD-type / G-protein beta WD-40 repeat / Small nuclear ribonucleoprotein E / CWF11 family / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / PRP8 domain IV core / Pre-mRNA splicing factor component Cdc5p/Cef1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Ribosomal protein S5 domain 2-type fold / WD40 repeat, conserved site / Small nuclear ribonucleoprotein Sm D2 / Tetratricopeptide repeat / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / BUD31/G10-related, conserved site / WD40-repeat-containing domain / Myb domain / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / P-loop containing nucleoside triphosphate hydrolase / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / HIT-like superfamily / RNA-binding domain superfamily / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / EF-G domain III/V-like / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Small nuclear ribonucleoprotein F / Pre-mRNA-processing-splicing factor 8 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / Pre-mRNA-processing factor 17 / Leucine-rich repeat domain superfamily / Intron-binding protein aquarius, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / mRNA splicing factor SYF2 / SKI-interacting protein, SKIP / Sm-like protein Lsm6/SmF / Zinc finger, CCCH-type superfamily / Homeobox-like domain superfamily / Small GTP-binding protein domain / Translation elongation factor EFG/EF2, domain IV / Cwf19-like protein, C-terminal domain-2 / Cwf19-like, C-terminal domain-1 / Pre-mRNA-splicing factor Cwf15/Cwc15 / Pre-mRNA-splicing factor SPF27 / Translation protein, beta-barrel domain superfamily / LSM domain superfamily / SKI-interacting protein SKIP, SNW domain / Tetratricopeptide-like helical domain superfamily / Ribonuclease H-like superfamily / PRO8NT domain / PROCN domain / Nucleotide-binding alpha-beta plait domain superfamily / PROCT domain / Tetratricopeptide repeat-containing domain / Translation elongation factor EFTu-like, domain 2 / U box domain / Peptidyl-prolyl cis-trans isomerase E / Ricin B, lectin domain / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Pre-mRNA-splicing factor 19 / RNA recognition motif domain / JAB1/MPN/MOV34 metalloenzyme domain / Zinc finger, CCCH-type / Elongation factor EFG, domain V-like / Transcription factor, GTP-binding domain / U2A'/phosphoprotein 32 family A, C-terminal / SANT/Myb domain / LSM domain, eukaryotic/archaea-type / Leucine-rich repeat / WD40 repeat / G10 protein / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / HAT (Half-A-TPR) repeat / WD40-repeat-containing domain superfamily / Cyclophilin-like domain superfamily / MPN domain / G10 protein / LSM domain / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Protein similar to CwfJ C-terminus 1 / Protein similar to CwfJ C-terminus 2 / Elongation Factor G, domain II / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / PROCT (NUC072) domain / U6-snRNA interacting domain of PrP8 / Elongation factor G, domain IV / U5-snRNA binding site 2 of PrP8 / SYF2 splicing factor / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / SKIP/SNW domain / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Cwf15/Cwc15 cell cycle control protein
Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein E / Protein BUD31 homolog / Pre-mRNA-splicing factor SPF27 / U2 small nuclear ribonucleoprotein A' / U2 small nuclear ribonucleoprotein B'' / Pre-mRNA-splicing factor SYF2 / Pre-mRNA-processing factor 17 ...Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein E / Protein BUD31 homolog / Pre-mRNA-splicing factor SPF27 / U2 small nuclear ribonucleoprotein A' / U2 small nuclear ribonucleoprotein B'' / Pre-mRNA-splicing factor SYF2 / Pre-mRNA-processing factor 17 / RNA helicase aquarius / Pleiotropic regulator 1 / Small nuclear ribonucleoprotein Sm D1 / 116 kDa U5 small nuclear ribonucleoprotein component / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor SYF1 / gb:20330981: / Peptidyl-prolyl cis-trans isomerase-like 1 / Peptidyl-prolyl cis-trans isomerase E / Pre-mRNA-processing factor 19 / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-splicing factor RBM22 / Crooked neck-like protein 1 / Small nuclear ribonucleoprotein Sm D3 / Cell division cycle 5-like protein / U5 small nuclear ribonucleoprotein 40 kDa protein / Pre-mRNA-processing-splicing factor 8 / Small nuclear ribonucleoprotein-associated protein / CWF19-like protein 2 / gb:340097: / SNW domain-containing protein 1
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.
Validation Report
SummaryFull reportAbout validation report
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

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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


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-I6P / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / MYO-INOSITOL 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 / Magnesium


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


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, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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