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- PDB-5mqf: Cryo-EM structure of a human spliceosome activated for step 2 of ... -

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Entry
Database: PDB / ID: 5mqf
TitleCryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)
Components
  • (Homo sapiens ...) x 2
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 5
  • (Small nuclear ribonucleoprotein ...) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • ATP-dependent RNA helicase DHX8
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • Eukaryotic initiation factor 4A-III
  • Human gene for small nuclear RNA U2 (snRNA U2)
  • Intron-binding protein aquarius
  • MINX pre-mRNA (intron)
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • U5 small nuclear ribonucleoprotein 40 kDa protein
KeywordsSPLICING / Spliceosome / pre-mRNA splicing / macromolecular complex
Function / homology
Function and homology information


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 / regulation of translation at postsynapse, modulating synaptic transmission / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / U2 snRNP binding / U7 snRNA binding ...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 / regulation of translation at postsynapse, modulating synaptic transmission / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / U2 snRNP binding / U7 snRNA binding / negative regulation of excitatory postsynaptic potential / histone pre-mRNA DCP binding / U7 snRNP / 3'-5' RNA helicase activity / generation of catalytic spliceosome for first transesterification step / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / histone pre-mRNA 3'end processing complex / alternative mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Deadenylation of mRNA / nuclear retinoic acid receptor binding / embryonic brain development / protein methylation / U12-type spliceosomal complex / poly(A) binding / 7-methylguanosine cap hypermethylation / M-decay: degradation of maternal mRNAs by maternally stored factors / U1 snRNP binding / RNA splicing, via transesterification reactions / mRNA 3'-end processing / sno(s)RNA-containing ribonucleoprotein complex / methylosome / ATP-dependent activity, acting on RNA / pICln-Sm protein complex / embryonic cranial skeleton morphogenesis / regulation of mRNA splicing, via spliceosome / oocyte development / C2H2 zinc finger domain binding / U2-type catalytic step 1 spliceosome / positive regulation of mRNA splicing, via spliceosome / pre-mRNA binding / snRNP binding / small nuclear ribonucleoprotein complex / telomerase holoenzyme complex / SMN-Sm protein complex / P granule / telomerase RNA binding / spliceosomal tri-snRNP complex / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / positive regulation of vitamin D receptor signaling pathway / commitment complex / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear vitamin D receptor binding / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U2-type catalytic step 2 spliceosome / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exploration behavior / U1 snRNP / NOTCH3 Intracellular Domain Regulates Transcription / U2-type prespliceosome / WD40-repeat domain binding / protein peptidyl-prolyl isomerization / inner cell mass cell proliferation / positive regulation of neurogenesis / ubiquitin-ubiquitin ligase activity / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / lipid biosynthetic process / cyclosporin A binding / Notch-HLH transcription pathway / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / spliceosomal complex assembly / mitotic G2 DNA damage checkpoint signaling / associative learning / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / blastocyst development / Prp19 complex / protein K63-linked ubiquitination / U5 snRNA binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein localization to nucleus / U5 snRNP / positive regulation of G1/S transition of mitotic cell cycle / embryonic organ development
Similarity search - Function
DHX8/ Prp22, DEXH-box helicase domain / : / : / HAT (Half-A-TPR) repeat / Prp19 WD40 domain / : / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain ...DHX8/ Prp22, DEXH-box helicase domain / : / : / HAT (Half-A-TPR) repeat / Prp19 WD40 domain / : / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / 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 / 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 / mRNA splicing factor Cwf21 domain / cwf21 domain / Pre-mRNA-processing factor 17 / U-box domain / : / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / G10 protein signature 2. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / BUD31/G10-related, conserved site / G10 protein signature 1. / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / DNA2/NAM7 helicase, helicase domain / : / AAA domain / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / 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 / DNA2/NAM7-like helicase / : / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Small ribonucleoprotein associated, SmB/SmN / Myb-like DNA-binding domain / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / U2 small nuclear ribonucleoprotein A' / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Small nuclear ribonucleoprotein D1 / U-box domain profile. / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Modified RING finger domain / U-box domain / Zinc finger, CCCH-type superfamily / zinc finger / Leucine-rich repeat / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Pre-mRNA-splicing factor Syf1-like / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / 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
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / : / Pleiotropic regulator 1 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor SPF27 ...: / : / 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' / 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 / SNW domain-containing protein 1 / ATP-dependent RNA helicase DHX8 / 116 kDa U5 small nuclear ribonucleoprotein component / 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 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 / Peptidyl-prolyl cis-trans isomerase-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsBertram, K. / Hartmuth, K. / Kastner, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 860 Germany
CitationJournal: Nature / Year: 2017
Title: Cryo-EM structure of a human spliceosome activated for step 2 of splicing.
Authors: Karl Bertram / Dmitry E Agafonov / Wen-Ti Liu / Olexandr Dybkov / Cindy L Will / Klaus Hartmuth / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human ...Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated from the catalytic centre by approximately 20 Å, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 Å from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C* complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.3Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: 116 kDa U5 small nuclear ribonucleoprotein component
C: SNW domain-containing protein 1
D: Pleiotropic regulator 1
E: Pre-mRNA-processing factor 17
F: U5 small nuclear ribonucleoprotein 40 kDa protein
G: Pre-mRNA-processing factor 19
H: Pre-mRNA-processing factor 19
I: Pre-mRNA-processing factor 19
J: Pre-mRNA-processing factor 19
K: Pre-mRNA-splicing factor SPF27
L: Cell division cycle 5-like protein
M: Pre-mRNA-splicing factor SYF1
N: Pre-mRNA-splicing factor SYF2
O: Crooked neck-like protein 1
P: Pre-mRNA-splicing factor RBM22
Q: Protein BUD31 homolog
R: Spliceosome-associated protein CWC15 homolog
S: Serine/arginine repetitive matrix protein 2
T: Pre-mRNA-splicing factor CWC22 homolog
U: Intron-binding protein aquarius
V: Peptidyl-prolyl cis-trans isomerase-like 1
W: U2 small nuclear ribonucleoprotein A'
X: U2 small nuclear ribonucleoprotein B''
a: Small nuclear ribonucleoprotein Sm D2
b: Small nuclear ribonucleoprotein F
c: Small nuclear ribonucleoprotein E
d: Small nuclear ribonucleoprotein G
e: Small nuclear ribonucleoprotein Sm D3
f: Small nuclear ribonucleoprotein-associated proteins B and B'
g: Small nuclear ribonucleoprotein Sm D1
h: Small nuclear ribonucleoprotein Sm D2
i: Small nuclear ribonucleoprotein F
j: Small nuclear ribonucleoprotein E
k: Small nuclear ribonucleoprotein G
l: Small nuclear ribonucleoprotein Sm D3
m: Small nuclear ribonucleoprotein-associated proteins B and B'
n: Small nuclear ribonucleoprotein Sm D1
o: Peptidyl-prolyl cis-trans isomerase E
p: Eukaryotic initiation factor 4A-III
q: ATP-dependent RNA helicase DHX8
Y: MINX pre-mRNA (intron)
Z: MINX pre-mRNA (intron)
2: Human gene for small nuclear RNA U2 (snRNA U2)
5: Homo sapiens U5 A small nuclear RNA
6: Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA


Theoretical massNumber of molelcules
Total (without water)2,666,32846
Polymers2,666,32846
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area65780 Å2
ΔGint-714 kcal/mol
Surface area486870 Å2
MethodPISA

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Components

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Protein , 14 types, 15 molecules ABCDFLOQRSUfmpq

#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
#2: 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
#3: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61610.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#4: Protein Pleiotropic regulator 1


Mass: 57379.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#6: 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
#9: 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
#12: 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
#14: 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
#15: 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
#16: 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
#18: Protein Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160 / Coordinate model: Cα atoms only


Mass: 173003.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60306
#27: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#30: 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 / Coordinate model: Cα atoms only


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
#31: Protein ATP-dependent RNA helicase DHX8 / DEAH box protein 8 / RNA helicase HRH1 / Coordinate model: Cα atoms only


Mass: 139251.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14562, RNA helicase

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

#5: 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
#7: Protein
Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / 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, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Pre-mRNA-splicing factor ... , 5 types, 5 molecules KMNPT

#8: 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
#10: 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 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
#13: 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
#17: 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 ... , 2 types, 2 molecules Vo

#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
#29: Protein Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E / Coordinate model: Cα atoms only


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

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


Mass: 28484.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09661
#21: 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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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahbicjdkelgn

#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#28: 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

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RNA chain , 2 types, 3 molecules YZ2

#32: RNA chain MINX pre-mRNA (intron)


Mass: 104019.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#33: RNA chain Human gene for small nuclear RNA U2 (snRNA U2)


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36516

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Homo sapiens ... , 2 types, 2 molecules 56

#34: RNA chain Homo sapiens U5 A small nuclear RNA


Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36515
#35: RNA chain Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: REF: 161087014

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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 C* Spliceosome, masked refinement / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 6.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Cs: 0.01 mm
Image recordingElectron dose: 2.1 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 17 / Used frames/image: 2-17

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136534 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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