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- PDB-8i0t: The cryo-EM structure of human Bact-III complex -

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Basic information

Entry
Database: PDB / ID: 8i0t
TitleThe cryo-EM structure of human Bact-III complex
Components
  • (Peptidyl-prolyl cis-trans isomerase-like ...) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 5
  • (Small nuclear ribonucleoprotein ...) x 6
  • (Splicing factor 3A subunit ...) x 3
  • (Splicing factor 3B subunit ...) x 5
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • PHD finger-like domain-containing protein 5A
  • Peptidyl-prolyl cis-trans isomerase E
  • Pleiotropic regulator 1
  • Pre-mRNA
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • RING finger protein 113A
  • RING-type E3 ubiquitin-protein ligase PPIL2
  • RNA helicase aquarius
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
KeywordsSPLICING / spliceosome / Bact complex / RNA splicing / PRP2 / branching
Function / homology
Function and homology information


negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step ...negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / B-WICH complex / regulation of vitamin D receptor signaling pathway / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / embryonic brain development / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / U1 snRNP binding / mRNA 3'-end processing / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / telomerase RNA binding / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / U4 snRNP / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Notch binding / RUNX3 regulates NOTCH signaling / SAGA complex / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / Basigin interactions / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / pattern recognition receptor activity / lipid biosynthetic process / positive regulation of neurogenesis / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / nuclear androgen receptor binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / SMAD binding / protein K63-linked ubiquitination / regulation of RNA splicing / antiviral innate immune response / mRNA 3'-splice site recognition / blastocyst development / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / proteasomal protein catabolic process / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / RNA processing
Similarity search - Function
PPIL4-like, cyclophilin domain / Cyclophilin-RNA interacting protein / Peptidyl-prolyl cis-trans isomerase like 2, U-box domain / Pre-mRNA-splicing factor CWC24-like / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Pre-mRNA-splicing factor SPF27 / : ...PPIL4-like, cyclophilin domain / Cyclophilin-RNA interacting protein / Peptidyl-prolyl cis-trans isomerase like 2, U-box domain / Pre-mRNA-splicing factor CWC24-like / : / : / 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 / SF3B4, RNA recognition motif 2 / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Cactus-binding C-terminus of cactin protein / : / Replication stress response SDE2 C-terminal / mRNA splicing factor Cwf21 domain / Splicing factor 3A subunit 1, ubiquitin domain / cwf21 domain / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / SF3A2 domain / : / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / STL11, N-terminal / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / U-box domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / : / SF3B4, RNA recognition motif 1 / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / WD repeat Prp46/PLRG1-like / Splicing factor 3A subunit 1 / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Splicing factor 3B, subunit 5 / BUD31/G10-related, conserved site / : / : / : / G10 protein signature 1. / G10 protein signature 2. / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / Splicing factor 3A subunit 1, conserved domain / SKIP/SNW domain / Pre-mRNA splicing factor PRP21 like protein / Myb-like DNA-binding domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / HAT (Half-A-TPR) repeat / Cwf15/Cwc15 cell cycle control protein / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Domain of unknown function DUF382 / Pre-mRNA-splicing factor Cwc2/Slt11 / Domain of unknown function (DUF382) / G10 protein / Pre-mRNA-splicing factor BUD31 / SWAP/Surp / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / SWAP/Surp superfamily / Surp module / pre-mRNA splicing factor component / Zinc-finger of C2H2 type / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / PHF5-like / PHF5-like protein / PSP, proline-rich / MIF4G domain / PSP / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Small ribonucleoprotein associated, SmB/SmN / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Small nuclear ribonucleoprotein D1 / U-box domain profile.
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / 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 / Splicing factor 3A subunit 3 / RING-type E3 ubiquitin-protein ligase PPIL2 / Splicing factor 3B subunit 2 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / Splicing factor 3B subunit 4 / Splicing factor 3A subunit 2 / Splicing factor 3A subunit 1 / Pre-mRNA-processing-splicing factor 8 / PHD finger-like domain-containing protein 5A / Peptidyl-prolyl cis-trans isomerase-like 4 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Splicing factor 3B subunit 5 / 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)
unidentified adenovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhan, X. / Lu, Y. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Molecular basis for the activation of human spliceosome
Authors: Zhan, X. / Lu, Y. / Shi, Y.
History
DepositionJan 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: U5 snRNA
C: 116 kDa U5 small nuclear ribonucleoprotein component
D: U5 small nuclear ribonucleoprotein 200 kDa helicase
E: U5 small nuclear ribonucleoprotein 40 kDa protein
F: U6 snRNA
G: Pre-mRNA
H: U2 snRNA
I: Pre-mRNA-splicing factor SYF1
J: Crooked neck-like protein 1
K: RING finger protein 113A
L: Cell division cycle 5-like protein
N: Protein BUD31 homolog
O: Pre-mRNA-splicing factor RBM22
P: Spliceosome-associated protein CWC15 homolog
Q: RNA helicase aquarius
R: SNW domain-containing protein 1
S: Peptidyl-prolyl cis-trans isomerase-like 1
T: Pleiotropic regulator 1
U: Serine/arginine repetitive matrix protein 2
V: Pre-mRNA-splicing factor CWC22 homolog
W: Pre-mRNA-processing factor 17
X: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
Y: Peptidyl-prolyl cis-trans isomerase-like 4
Z: Pre-mRNA-splicing factor SPF27
1: Splicing factor 3B subunit 1
3: Splicing factor 3B subunit 3
p: U2 small nuclear ribonucleoprotein B''
w: Splicing factor 3A subunit 3
2: Splicing factor 3B subunit 2
4: Splicing factor 3B subunit 4
7: PHD finger-like domain-containing protein 5A
5: Splicing factor 3B subunit 5
y: Peptidyl-prolyl cis-trans isomerase E
v: Splicing factor 3A subunit 2
o: U2 small nuclear ribonucleoprotein A'
h: Small nuclear ribonucleoprotein Sm D2
i: Small nuclear ribonucleoprotein F
m: Small nuclear ribonucleoprotein-associated proteins B and B'
l: Small nuclear ribonucleoprotein Sm D3
k: Small nuclear ribonucleoprotein G
j: Small nuclear ribonucleoprotein E
n: Small nuclear ribonucleoprotein Sm D1
u: Splicing factor 3A subunit 1
a: Small nuclear ribonucleoprotein-associated proteins B and B'
b: Small nuclear ribonucleoprotein Sm D1
c: Small nuclear ribonucleoprotein Sm D2
d: Small nuclear ribonucleoprotein F
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein G
g: Small nuclear ribonucleoprotein Sm D3
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
9: RING-type E3 ubiquitin-protein ligase PPIL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,480,41472
Polymers3,478,60356
Non-polymers1,81116
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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Protein , 15 types, 16 molecules ACJKLNPQRTU7yma9

#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 / SNU114 / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / ...SNU114 / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#10: Protein Crooked neck-like protein 1 / SYF3 / 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
#11: Protein RING finger protein 113A


Mass: 38847.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15541
#12: Protein Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#13: Protein Protein BUD31 homolog / 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 RNA helicase aquarius


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


Mass: 61690.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#19: 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
#20: Protein Serine/arginine repetitive matrix protein 2 / Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related ...Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related nuclear matrix protein of 300 kDa


Mass: 300255.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35
#32: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A


Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0
#34: 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
#39: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / SmB / 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
#46: Protein RING-type E3 ubiquitin-protein ligase PPIL2 / Probable inactive peptidyl-prolyl cis-trans isomerase-like 2 / PPIase / Rotamase PPIL2


Mass: 58910.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q13356, RING-type E3 ubiquitin transferase

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RNA chain , 4 types, 4 molecules BFGH

#2: RNA chain U5 snRNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981
#6: RNA chain U6 snRNA


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


Mass: 70435.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus
#8: RNA chain U2 snRNA


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

#4: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / BRR2 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#5: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / SNR40 / U5-40K / U5 snRNP-specific 40 kDa protein


Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7

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

#9: Protein Pre-mRNA-splicing factor SYF1


Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#14: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22


Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#21: 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
#23: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / ATP-dependent RNA helicase #3 / DEAH-box protein 16


Mass: 119443.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60231, RNA helicase
#25: 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 isomerase-like ... , 2 types, 2 molecules SY

#18: 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
#24: Protein Peptidyl-prolyl cis-trans isomerase-like 4 / PPIase / Cyclophilin-like protein PPIL4 / Rotamase PPIL4


Mass: 57324.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUA2, peptidylprolyl isomerase

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

#22: Protein Pre-mRNA-processing factor 17 / 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
#45: Protein
Pre-mRNA-processing factor 19 / 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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Splicing factor 3B subunit ... , 5 types, 5 molecules 13245

#26: Protein Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155


Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533
#27: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393
#30: Protein Splicing factor 3B subunit 2 / Pre-mRNA-splicing factor SF3b 145 kDa subunit / SF3b145


Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435
#31: Protein Splicing factor 3B subunit 4 / Pre-mRNA-splicing factor SF3b 49 kDa subunit


Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15427
#33: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5

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

#28: Protein U2 small nuclear ribonucleoprotein B'' / U2-B" / U2 / 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
#36: Protein U2 small nuclear ribonucleoprotein A' / U2-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

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Splicing factor 3A subunit ... , 3 types, 3 molecules wvu

#29: Protein Splicing factor 3A subunit 3 / SF3a60 / Spliceosome-associated protein 61 / SAP 61


Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12874
#35: Protein Splicing factor 3A subunit 2 / SF3a66


Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15428
#44: Protein Splicing factor 3A subunit 1 / SF3a120


Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459

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

#37: 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
#38: 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
#40: Protein Small nuclear ribonucleoprotein Sm D3 / SmD3 / 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
#41: 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
#42: 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
#43: 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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Non-polymers , 4 types, 16 molecules

#47: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#48: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#49: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: The human Bact-III complex / Type: COMPLEX
Entity ID: #1-#3, #5, #21, #11, #6, #8, #26-#27, #10, #12, #15, #28-#29, #16, #9, #30-#33, #17, #19, #34-#35, #7, #14, #13, #20, #36, #44, #39, #43, #37-#38, #42, #41, #40, #4, #22-#24, #18, #45, #25, #46
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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111205 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011123326
ELECTRON MICROSCOPYf_angle_d0.979170015
ELECTRON MICROSCOPYf_dihedral_angle_d16.10523090
ELECTRON MICROSCOPYf_chiral_restr0.05619765
ELECTRON MICROSCOPYf_plane_restr0.00721490

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