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- PDB-6ahd: The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B compl... -

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Entry
Database: PDB / ID: 6ahd
TitleThe Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution
Components
  • (Small nuclear ribonucleoprotein Sm ...) x 3
  • (Splicing factor 3A subunit ...) x 3
  • (Splicing factor 3B subunit ...) x 2
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U4/U6 small nuclear ribonucleoprotein ...) x 3
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Brr2, U5 small nuclear ribonucleoprotein 200 kDa helicase
  • Microfibrillar-associated protein 1
  • NHP2-like protein 1
  • PHD finger-like domain-containing protein 5A
  • Peptidyl-prolyl cis-trans isomerase H
  • Pre-mRNA-processing factor 6
  • Pre-mRNA-processing-splicing factor 8
  • Pre-mRNA-splicing factor 38A
  • SF3b145, Splicing factor 3B subunit 2
  • SF3b14a, Splicing factor 3B subunit 6
  • SF3b49, Splicing factor 3B subunit 4
  • SF3b5, Splicing factor 3B subunit 5
  • SmB
  • SmE
  • SmF
  • Small nuclear ribonucleoprotein G
  • Thioredoxin-like protein 4A
  • U2snRNA
  • U4/U6.U5 tri-snRNP-associated protein 1
  • U4snRNA
  • U5 small nuclear ribonucleoprotein 40 kDa protein
  • U5snRNA
  • U6snRNA
  • Ubiquitin-like protein 5
  • WD40 repeat-containing protein SMU1
  • WW domain-binding protein 4
  • Zinc finger matrin-type protein 2
  • pre-mRNAPrimary transcript
KeywordsSPLICING / Spliceosome
Function / homology
Function and homology information


spliceosomal snRNP complex / Lsm2-8 complex / U6 snRNA 3'-end binding / ribonucleoprotein complex localization / microfibril / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding ...spliceosomal snRNP complex / Lsm2-8 complex / U6 snRNA 3'-end binding / ribonucleoprotein complex localization / microfibril / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U11/U12 snRNP / box C/D sno(s)RNA binding / snRNP binding / U6 snRNP / PH domain binding / U7 snRNA binding / histone pre-mRNA DCP binding / dense fibrillar component / U7 snRNP / B-WICH complex / U4/U6 snRNP / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / splicing factor binding / methylosome / protein methylation / U12-type spliceosomal complex / P-body assembly / 7-methylguanosine cap hypermethylation / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / RNA splicing, via transesterification reactions / blastocyst formation / spliceosomal tri-snRNP complex / U4 snRNP / small nuclear ribonucleoprotein complex / P granule / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / : / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / box C/D snoRNP assembly / commitment complex / U2-type catalytic step 2 spliceosome / rRNA modification in the nucleus and cytosol / proline-rich region binding / U2 snRNP / SAGA complex / nuclear-transcribed mRNA catabolic process / U3 snoRNA binding / positive regulation of transcription by RNA polymerase III / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / tRNA processing / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of protein targeting to mitochondrion / precatalytic spliceosome / spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / single fertilization / mRNA catabolic process / MLL1 complex / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / regulation of DNA repair / positive regulation of viral genome replication / Cajal body / spliceosomal snRNP assembly / U2 snRNA binding / U6 snRNA binding / ribonucleoprotein complex binding / RNA processing / pre-mRNA intronic binding / protein peptidyl-prolyl isomerization / maturation of SSU-rRNA / U1 snRNA binding / translation elongation factor activity / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome
Similarity search - Function
WW domain-binding protein 4 / WD40 repeat-containing protein SMU1 / LisH-like dimerisation domain / Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / PRP4-like superfamily / Ubiquitin-like modifier Hub1/Ubl5 / Microfibril-associated/Pre-mRNA processing ...WW domain-binding protein 4 / WD40 repeat-containing protein SMU1 / LisH-like dimerisation domain / Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / PRP4-like superfamily / Ubiquitin-like modifier Hub1/Ubl5 / Microfibril-associated/Pre-mRNA processing / pre-mRNA processing factor 4 (PRP4) like / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / PRP38 family / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / PWI domain superfamily / PWI domain / PWI domain profile. / SF3B6, RNA recognition motif / U1-C, C2H2-type zinc finger / U1 zinc finger / Splicing factor 3A subunit 1, ubiquitin domain / SF3B4, RNA recognition motif 2 / C-terminal to LisH motif. / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Pre-mRNA processing factor 4 (PRP4)-like / Splicing Factor Motif, present in Prp18 and Pr04 / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / Sm-like protein Lsm8 / pre-mRNA processing factor 3 domain / PWI domain / : / Replication stress response SDE2 C-terminal / PWI, domain in splicing factors / Cactus-binding C-terminus of cactin protein / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / U6 snRNA-associated Sm-like protein Lsm1/8 / Dim1 family / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Mitosis protein DIM1 / Mitosis protein DIM1 / Sm-like protein Lsm7 / PRP1 splicing factor, N-terminal / Sm-like protein LSm5 / Sm-like protein Lsm3 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / U6 snRNA-associated Sm-like protein Lsm3 / PRP1 splicing factor, N-terminal / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / SF3A2 domain / U2 small nuclear ribonucleoprotein A' / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3B4, RNA recognition motif 1 / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / Splicing factor 3B, subunit 5 / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / Zinc-finger of C2H2 type / PHF5-like / PHF5-like protein / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Matrin/U1-C, C2H2-type zinc finger / Splicing factor 3B subunit 1-like / Zinc finger matrin-type profile. / Lissencephaly type-1-like homology motif / Small nuclear ribonucleoprotein D1 / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Pre-mRNA-splicing factor Syf1-like / NOSIC
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6.U5 tri-snRNP-associated protein 1 ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6.U5 tri-snRNP-associated protein 1 / U4/U6 small nuclear ribonucleoprotein Prp3 / Peptidyl-prolyl cis-trans isomerase H / Splicing factor 3B subunit 1 / WW domain-binding protein 4 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / U6 snRNA-associated Sm-like protein LSm8 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Microfibrillar-associated protein 1 / NHP2-like protein 1 / Small nuclear ribonucleoprotein G / U6 snRNA-associated Sm-like protein LSm3 / U6 snRNA-associated Sm-like protein LSm6 / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Thioredoxin-like protein 4A / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / 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 / WD40 repeat-containing protein SMU1 / Pre-mRNA-processing-splicing factor 8 / PHD finger-like domain-containing protein 5A / Pre-mRNA-splicing factor 38A / U4/U6 small nuclear ribonucleoprotein Prp31 / U5 small nuclear ribonucleoprotein 40 kDa protein / Zinc finger matrin-type protein 2 / Splicing factor 3B subunit 5 / Ubiquitin-like protein 5 / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm2 / Splicing factor 3B subunit 6 / U6 snRNA-associated Sm-like protein LSm5 / U6 snRNA-associated Sm-like protein LSm4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhan, X. / Yan, C. / Zhang, X. / 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: 2018
Title: Structures of the human pre-catalytic spliceosome and its precursor spliceosome.
Authors: Xiechao Zhan / Chuangye Yan / Xiaofeng Zhang / Jianlin Lei / Yigong Shi /
Abstract: The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B complex). The pre-B-to-B and B-to-B transitions are ...The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B complex). The pre-B-to-B and B-to-B transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5'-exon is anchored to loop I of U5 snRNA, and the 5'-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human spliceosome.
History
DepositionAug 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.3Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Jun 30, 2021Group: Database references / Source and taxonomy / Category: entity_src_nat / struct_ref / Item: _struct_ref.entity_id

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Structure visualization

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
I: U4snRNA
B: U5snRNA
F: U6snRNA
G: pre-mRNA
O: Thioredoxin-like protein 4A
C: 116 kDa U5 small nuclear ribonucleoprotein component
N: Pre-mRNA-processing factor 6
M: NHP2-like protein 1
L: U4/U6 small nuclear ribonucleoprotein Prp31
9: U4/U6.U5 tri-snRNP-associated protein 1
J: U4/U6 small nuclear ribonucleoprotein Prp3
a: SmB
b: Small nuclear ribonucleoprotein Sm D1
c: Small nuclear ribonucleoprotein Sm D2
d: SmE
e: SmF
f: Small nuclear ribonucleoprotein G
g: Small nuclear ribonucleoprotein Sm D3
E: U5 small nuclear ribonucleoprotein 40 kDa protein
X: WW domain-binding protein 4
W: Peptidyl-prolyl cis-trans isomerase H
A0: Ubiquitin-like protein 5
0: Microfibrillar-associated protein 1
Z: Pre-mRNA-splicing factor 38A
8: Zinc finger matrin-type protein 2
Y: WD40 repeat-containing protein SMU1
H: U2snRNA
h: Small nuclear ribonucleoprotein Sm D3
i: SmB
j: Small nuclear ribonucleoprotein Sm D1
k: Small nuclear ribonucleoprotein Sm D2
l: SmE
m: SmF
n: Small nuclear ribonucleoprotein G
o: U2 small nuclear ribonucleoprotein A'
p: U2 small nuclear ribonucleoprotein B''
u: Splicing factor 3A subunit 1
v: Splicing factor 3A subunit 2
w: Splicing factor 3A subunit 3
q: U6 snRNA-associated Sm-like protein LSm2
r: U6 snRNA-associated Sm-like protein LSm3
s: U6 snRNA-associated Sm-like protein LSm4
t: U6 snRNA-associated Sm-like protein LSm5
x: U6 snRNA-associated Sm-like protein LSm6
y: U6 snRNA-associated Sm-like protein LSm7
z: U6 snRNA-associated Sm-like protein LSm8
P: Small nuclear ribonucleoprotein Sm D2
Q: SmE
R: SmF
S: Small nuclear ribonucleoprotein G
T: Small nuclear ribonucleoprotein Sm D3
U: SmB
V: Small nuclear ribonucleoprotein Sm D1
K: U4/U6 small nuclear ribonucleoprotein Prp4
1: Splicing factor 3B subunit 1
3: Splicing factor 3B subunit 3
5: SF3b14a, Splicing factor 3B subunit 6
6: PHD finger-like domain-containing protein 5A
7: SF3b5, Splicing factor 3B subunit 5
2: SF3b145, Splicing factor 3B subunit 2
4: SF3b49, Splicing factor 3B subunit 4
D: Brr2, U5 small nuclear ribonucleoprotein 200 kDa helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,671,16566
Polymers2,669,95763
Non-polymers1,2083
Water0
1


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

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Components

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Protein , 24 types, 32 molecules AOCNM9aiUdlQemRfnSEXWA00Z8Y56724D

#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
#6: Protein Thioredoxin-like protein 4A / DIM1 protein homolog / Spliceosomal U5 snRNP-specific 15 kDa protein / Thioredoxin-like U5 snRNP ...DIM1 protein homolog / Spliceosomal U5 snRNP-specific 15 kDa protein / Thioredoxin-like U5 snRNP protein U5-15kD


Mass: 16807.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83876
#7: 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
#8: Protein Pre-mRNA-processing factor 6 / Androgen receptor N-terminal domain-transactivating protein 1 / ANT-1 / PRP6 homolog / U5 snRNP- ...Androgen receptor N-terminal domain-transactivating protein 1 / ANT-1 / PRP6 homolog / U5 snRNP-associated 102 kDa protein / U5-102 kDa protein


Mass: 107092.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O94906
#9: Protein NHP2-like protein 1 / High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog / hSNU13 / U4/U6.U5 ...High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog / hSNU13 / U4/U6.U5 small nuclear ribonucleoprotein SNU13 / U4/U6.U5 tri-snRNP 15.5 kDa protein


Mass: 14191.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55769
#11: Protein U4/U6.U5 tri-snRNP-associated protein 1 / SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / hSART-1 / U4/U6. ...SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / hSART-1 / U4/U6.U5 tri-snRNP-associated 110 kDa protein


Mass: 90414.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43290
#13: Protein SmB


Mass: 23686.004 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#16: Protein SmE


Mass: 9734.171 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#17: Protein SmF


Mass: 10817.601 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#18: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308
#20: 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
#21: Protein WW domain-binding protein 4 / WBP-4 / Formin-binding protein 21 / WW domain-containing-binding protein 4


Mass: 42575.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75554
#22: Protein Peptidyl-prolyl cis-trans isomerase H / PPIase H / Rotamase H / Small nuclear ribonucleoprotein particle-specific cyclophilin H / CypH / U- ...PPIase H / Rotamase H / Small nuclear ribonucleoprotein particle-specific cyclophilin H / CypH / U-snRNP-associated cyclophilin SnuCyp-20 / USA-CYP


Mass: 19230.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43447, peptidylprolyl isomerase
#23: Protein Ubiquitin-like protein 5


Mass: 8560.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZL1
#24: Protein Microfibrillar-associated protein 1 / Spliceosome B complex protein MFAP1


Mass: 52050.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55081
#25: Protein Pre-mRNA-splicing factor 38A


Mass: 37563.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NAV1
#26: Protein Zinc finger matrin-type protein 2


Mass: 23664.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96NC0
#27: Protein WD40 repeat-containing protein SMU1 / Smu-1 suppressor of mec-8 and unc-52 protein homolog


Mass: 57616.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q2TAY7
#44: Protein SF3b14a, Splicing factor 3B subunit 6 / Spliceosome-associated protein / 14-kDa Splicing factor 3b / subunit 6


Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B4
#45: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b


Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0
#46: Protein SF3b5, Splicing factor 3B subunit 5 / 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, UniProt: O43172*PLUS
#47: Protein SF3b145, Splicing factor 3B subunit 2 / Pre-mRNA-splicing factor SF3b 145 kDa subunit / Spliceosome-associated protein 145 / SAP 145


Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435, UniProt: O75533*PLUS
#48: Protein SF3b49, Splicing factor 3B subunit 4 / Pre-mRNA-splicing factor SF3b 49 kDa subunit / Spliceosome-associated protein 49 / SAP 49


Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15427
#49: Protein Brr2, U5 small nuclear ribonucleoprotein 200 kDa helicase / 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

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RNA chain , 5 types, 5 molecules IBFGH

#2: RNA chain U4snRNA


Mass: 46181.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 340142
#3: 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
#4: RNA chain U6snRNA


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


Mass: 87892.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#28: 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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U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules LJK

#10: Protein U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP ...Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP 61 kDa protein / hPrp31


Mass: 55528.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WWY3
#12: Protein U4/U6 small nuclear ribonucleoprotein Prp3 / Pre-mRNA-splicing factor 3 / hPrp3 / U4/U6 snRNP 90 kDa protein


Mass: 77669.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43395
#41: Protein U4/U6 small nuclear ribonucleoprotein Prp4 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 58536.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43172

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Small nuclear ribonucleoprotein Sm ... , 3 types, 9 molecules bjVckPghT

#14: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#15: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#19: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318

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

#31: Protein Splicing factor 3A subunit 1 / SF3a120 / Spliceosome-associated protein 114 / SAP 114


Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459
#32: Protein Splicing factor 3A subunit 2 / SF3a66 / Spliceosome-associated protein 62 / SAP 62


Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15428
#33: 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

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U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules qrstxyz

#34: Protein U6 snRNA-associated Sm-like protein LSm2 / Protein G7b / Small nuclear ribonuclear protein D homolog / snRNP core Sm-like protein Sm-x5


Mass: 10847.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y333
#35: Protein U6 snRNA-associated Sm-like protein LSm3


Mass: 11859.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62310
#36: Protein U6 snRNA-associated Sm-like protein LSm4 / Glycine-rich protein / GRP


Mass: 15375.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y4Z0
#37: Protein U6 snRNA-associated Sm-like protein LSm5


Mass: 9945.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y4Y9
#38: Protein U6 snRNA-associated Sm-like protein LSm6


Mass: 9139.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62312
#39: Protein U6 snRNA-associated Sm-like protein LSm7


Mass: 11617.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UK45
#40: Protein U6 snRNA-associated Sm-like protein LSm8


Mass: 10410.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95777

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Splicing factor 3B subunit ... , 2 types, 2 molecules 13

#42: Protein Splicing factor 3B subunit 1 / Prp4 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533
#43: Protein Splicing factor 3B subunit 3 / SF3b155 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393

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Non-polymers , 3 types, 3 molecules

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


Mass: 660.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H18O24P6 / References: UniProt: Q15393*PLUS
#51: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H16N5O14P3 / References: UniProt: Q9Y3B4*PLUS / Comment: GTP, energy-carrying molecule*YM
#52: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / References: UniProt: Q13435*PLUS

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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 Pre-catalytic spliceosome (B complex) / Type: COMPLEX / Entity ID: #1-#47 / 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137853 / Symmetry type: POINT

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