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- PDB-7a5p: Human C Complex Spliceosome - Medium-resolution PERIPHERY -

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Basic information

Entry
Database: PDB / ID: 7a5p
TitleHuman C Complex Spliceosome - Medium-resolution PERIPHERY
Components
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 7
  • (Small nuclear ribonucleoprotein ...) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • Eukaryotic initiation factor 4A-III
  • Intron-binding protein aquarius
  • Peptidyl-prolyl cis-trans isomerase E
  • Peptidylprolyl isomerase domain and WD repeat-containing protein 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein FRG1
  • Protein mago nashi homolog
  • RNA-binding protein 8A
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Splicing factor YJU2
  • U2 snRNA
  • U5 small nuclear ribonucleoprotein 200 kDa helicase
  • U5 snRNA
  • U6 snRNA
  • UNKNOWN
  • WD repeat-containing protein 70
  • pre-mRNA
KeywordsSPLICING / human C complex / spliceosome / hC / human step 1 spliceosome
Function / homology
Function and homology information


striated muscle dense body / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / cellular response to selenite ion / exon-exon junction complex / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of vitamin D receptor signaling pathway / selenocysteine insertion sequence binding / mRNA metabolic process / regulation of translation at postsynapse, modulating synaptic transmission ...striated muscle dense body / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / cellular response to selenite ion / exon-exon junction complex / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of vitamin D receptor signaling pathway / selenocysteine insertion sequence binding / mRNA metabolic process / regulation of translation at postsynapse, modulating synaptic transmission / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / generation of catalytic spliceosome for first transesterification step / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / 3'-5' RNA helicase activity / cis assembly of pre-catalytic spliceosome / histone pre-mRNA 3'end processing complex / nuclear histone mRNA catabolic process / embryonic cranial skeleton morphogenesis / U4atac snRNP / U4atac/U6atac snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / Deadenylation of mRNA / C2H2 zinc finger domain binding / U11/U12 snRNP / negative regulation of excitatory postsynaptic potential / poly(A) binding / U4atac/U6atac x U5 tri-snRNP complex / embryonic brain development / 7-methylguanosine cap hypermethylation / U12-type spliceosomal complex / nuclear retinoic acid receptor binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / post-spliceosomal complex / positive regulation of mRNA splicing, via spliceosome / RNA splicing, via transesterification reactions / pICln-Sm protein complex / snRNP binding / mRNA 3'-end processing / methylosome / U12-type catalytic step 2 spliceosome / post-mRNA release spliceosomal complex / muscle organ development / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / U12-type precatalytic spliceosome / spliceosomal tri-snRNP complex / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation of vitamin D receptor signaling pathway / RNA Polymerase II Transcription Termination / commitment complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / P granule / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Notch binding / U2-type spliceosomal complex / nuclear vitamin D receptor binding / telomerase holoenzyme complex / U2-type prespliceosome assembly / Transport of Mature mRNA derived from an Intron-Containing Transcript / NOTCH4 Intracellular Domain Regulates Transcription / telomerase RNA binding / pre-mRNA binding / U4/U6 snRNP / U2-type catalytic step 2 spliceosome / positive regulation of neurogenesis / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U1 snRNP / U2 snRNP / NOTCH3 Intracellular Domain Regulates Transcription / U2-type catalytic step 1 spliceosome / protein methylation / exploration behavior / U4 snRNP / mRNA stabilization / U2-type prespliceosome / mRNA cis splicing, via spliceosome / nuclear androgen receptor binding / cyclosporin A binding / K63-linked polyubiquitin modification-dependent protein binding / generation of catalytic spliceosome for second transesterification step / ubiquitin-ubiquitin ligase activity / Notch-HLH transcription pathway / Formation of paraxial mesoderm / regulation of alternative mRNA splicing, via spliceosome / precatalytic spliceosome / positive regulation of transforming growth factor beta receptor signaling pathway / WD40-repeat domain binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / mRNA 3'-splice site recognition / SMAD binding
Similarity search - Function
: / Protein FRG1 / FRG1-like domain / Splicing factor Yju2 / Saf4/Yju2 protein / Saf4/Yju2 protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi protein / Mago nashi superfamily ...: / Protein FRG1 / FRG1-like domain / Splicing factor Yju2 / Saf4/Yju2 protein / Saf4/Yju2 protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi protein / Mago nashi superfamily / Mago nashi protein / HAT (Half-A-TPR) repeat / Actin-crosslinking / : / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / Prp19 WD40 domain / : / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / RBM22 CCCH zinc finger 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) / mRNA splicing factor SYF2 / SYF2 splicing factor / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / Helix hairpin bin domain superfamily / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / : / : / cwf21 domain / UPF1-type helicase core domain profile. / mRNA splicing factor Cwf21 domain / Pre-mRNA-processing factor 17 / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / Prp19/Pso4-like / : / STL11, N-terminal / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / DNA2/NAM7 helicase, helicase domain / : / AAA domain / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / Pre-mRNA-splicing factor Cwc2/Slt11 / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / U-box domain / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / pre-mRNA splicing factor component / Initiation factor eIF-4 gamma, MA3 / : / : / MA3 domain / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / DNA2/NAM7-like helicase / : / MIF4G domain / Small ribonucleoprotein associated, SmB/SmN / U2 small nuclear ribonucleoprotein A' / Myb-like DNA-binding domain / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Spt5 C-terminal domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / Spt5 C-terminal nonapeptide repeat binding Spt4 / MIF4G-like, type 3 / Small nuclear ribonucleoprotein D1 / : / Pre-mRNA-splicing helicase BRR2 plug domain / Brr2, N-terminal helicase PWI domain / N-terminal helicase PWI domain / : / Winged Helix-turn-helix domain / Sec63 Brl domain / Zinc finger, CCCH-type superfamily / U-box domain profile. / Leucine-rich repeat / : / zinc finger / Pre-mRNA-splicing factor Syf1-like / Modified RING finger domain / U-box domain / Sec63 domain / Sec63 Brl domain
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / 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 ...: / : / RNA / RNA (> 10) / RNA (> 100) / 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 mago nashi 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 / Protein FRG1 / Pre-mRNA-processing-splicing factor 8 / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / 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 / WD repeat-containing protein 70 / Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase E / Serine/arginine repetitive matrix protein 2 / RNA-binding protein 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsBertram, K. / Kastner, B.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SFB 860 Germany
CitationJournal: Mol Cell / Year: 2020
Title: Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome.
Authors: Karl Bertram / Leyla El Ayoubi / Olexandr Dybkov / Dmitry E Agafonov / Cindy L Will / Klaus Hartmuth / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core ...Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core resolution and 4.5-5.7 Å at its periphery, and aided by protein crosslinking we determine its molecular architecture. Our structure provides additional insights into the spliceosome's architecture between the catalytic steps of splicing, and how proteins aid formation of the spliceosome's catalytically active RNP (ribonucleoprotein) conformation. It reveals the spatial organization of the metazoan-specific proteins PPWD1, WDR70, FRG1, and CIR1 in human C complexes, indicating they stabilize functionally important protein domains and RNA structures rearranged/repositioned during the B to C transition. Structural comparisons with human B, C, and P complexes reveal an intricate cascade of RNP rearrangements during splicing catalysis, with intermediate RNP conformations not found in yeast, and additionally elucidate the structural basis for the sequential recruitment of metazoan-specific spliceosomal proteins.
History
DepositionAug 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
2: U2 snRNA
5: U5 snRNA
6: U6 snRNA
8: UNKNOWN
A: Pre-mRNA-processing-splicing factor 8
C: SNW domain-containing protein 1
E: Pre-mRNA-processing factor 17
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
S: Serine/arginine repetitive matrix protein 2
T: Pre-mRNA-splicing factor CWC22 homolog
U: Intron-binding protein aquarius
W: U2 small nuclear ribonucleoprotein A'
X: U2 small nuclear ribonucleoprotein B''
Y: pre-mRNA
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
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
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: WD repeat-containing protein 70
q: U5 small nuclear ribonucleoprotein 200 kDa helicase
r: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
s: Pre-mRNA-splicing factor ISY1 homolog
u: Splicing factor YJU2
v: Protein mago nashi homolog
w: RNA-binding protein 8A
x: Protein FRG1
y: Eukaryotic initiation factor 4A-III
z: Peptidylprolyl isomerase domain and WD repeat-containing protein 1


Theoretical massNumber of molelcules
Total (without water)3,093,74048
Polymers3,093,74048
Non-polymers00
Water00
1


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

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Components

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RNA chain , 4 types, 4 molecules 256Y

#1: RNA chain U2 snRNA


Mass: 312349.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36516
#2: RNA chain U5 snRNA


Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36515
#3: RNA chain U6 snRNA


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: HeLa S3
#20: RNA chain pre-mRNA


Mass: 103979.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: HeLa S3

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Protein , 17 types, 18 molecules 8ACLOSUbmopquvwxyz

#4: Protein UNKNOWN


Mass: 17379.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: HeLa S3
#5: 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
#6: 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
#10: 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
#13: 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
#15: 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
#17: Protein Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 173331.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60306, RNA helicase
#22: 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
#28: 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
#29: Protein WD repeat-containing protein 70


Mass: 73306.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW82
#30: 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
#33: Protein Splicing factor YJU2 / 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
#34: Protein Protein mago nashi homolog


Mass: 17189.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61326
#35: 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
#36: Protein Protein FRG1 / FSHD region gene 1 protein


Mass: 29227.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14331
#37: 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
#38: 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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Pre-mRNA-processing factor ... , 2 types, 5 molecules EGHIJ

#7: 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
#8: 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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Pre-mRNA-splicing factor ... , 7 types, 7 molecules KMNPTrs

#9: 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
#11: 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
#12: 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
#14: 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
#16: 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
#31: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / ATP-dependent RNA helicase DHX38 / DEAH box protein 38


Mass: 140777.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92620, RNA helicase
#32: Protein Pre-mRNA-splicing factor ISY1 homolog


Mass: 33046.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULR0

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

#18: 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
#19: 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 alcndhejfigk

#21: 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
#23: 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
#24: 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
#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 F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEEEDGEMRE
Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#27: 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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Details

Has protein modificationY

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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 Complex Spliceosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa S3
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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
Image recordingElectron dose: 6 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5 Å / Resolution method: OTHER / Num. of particles: 69000 / Symmetry type: POINT

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