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- PDB-5o9z: Cryo-EM structure of a pre-catalytic human spliceosome primed for... -

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Entry
Database: PDB / ID: 5o9z
TitleCryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex)
Components
  • (Homo sapiens ...) x 3
  • (Small nuclear ribonucleoprotein ...) x 6
  • (Splicing factor 3B subunit ...) x 3
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U4/U6 small nuclear ribonucleoprotein ...) x 3
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Human gene for small nuclear RNA U2 (snRNA U2)
  • MINX pre-mRNA
  • 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
  • Protein Red
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Thioredoxin-like protein 4A
  • U4/U6.U5 tri-snRNP-associated protein 1
  • WD40 repeat-containing protein SMU1
  • WW domain-binding protein 4
  • Zinc finger matrin-type protein 2
KeywordsSPLICING / Spliceosome / pre-mRNA splicing / macromolecular complex
Function / homology
Function and homology information


microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding ...microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / 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 / U6 snRNP / box C/D sno(s)RNA binding / U11/U12 snRNP / PH domain binding / dense fibrillar component / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / 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 / box C/D methylation guide snoRNP complex / protein methylation / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / protein localization to kinetochore / U1 snRNP binding / pICln-Sm protein complex / P-body assembly / sno(s)RNA-containing ribonucleoprotein complex / snRNP binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / proline-rich region binding / mRNA cis splicing, via spliceosome / U3 snoRNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / box C/D snoRNP assembly / U4 snRNP / U2 snRNP / SAGA complex / rRNA modification in the nucleus and cytosol / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / U2-type prespliceosome / tRNA processing / regulation of alternative mRNA splicing, via spliceosome / precatalytic spliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / mitotic spindle assembly checkpoint signaling / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / mRNA catabolic process / regulation of RNA splicing / nuclear-transcribed mRNA catabolic process / protein peptidyl-prolyl isomerization / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / U5 snRNA binding / U5 snRNP / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of viral genome replication / U2 snRNA binding / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of DNA repair / Cajal body / RNA processing / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA Splicing - Major Pathway / RNA splicing
Similarity search - Function
Protein RED, C-terminal / RED-like, N-terminal / Protein Red-like / RED-like protein C-terminal region / RED-like protein N-terminal region / WD40 repeat-containing protein SMU1 / WW domain-binding protein 4 / Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal ...Protein RED, C-terminal / RED-like, N-terminal / Protein Red-like / RED-like protein C-terminal region / RED-like protein N-terminal region / WD40 repeat-containing protein SMU1 / WW domain-binding protein 4 / 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 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / : / LisH-like dimerisation domain / Pre-mRNA-splicing factor 38 / PRP38 family / U1-C, C2H2-type zinc finger / U1 zinc finger / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Sm-like protein Lsm8 / PWI domain superfamily / PWI domain / PWI domain profile. / U6 snRNA-associated Sm-like protein Lsm1/8 / Pre-mRNA processing factor 4 (PRP4)-like / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Splicing Factor Motif, present in Prp18 and Pr04 / Sm-like protein Lsm7 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / pre-mRNA processing factor 3 domain / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / PWI domain / PWI, domain in splicing factors / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / : / Lissencephaly type-1-like homology motif / PHF5-like / PHF5-like protein / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Small ribonucleoprotein associated, SmB/SmN / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Small nuclear ribonucleoprotein D1 / H/ACA ribonucleoprotein complex, subunit Nhp2-like / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / PPP2R1A-like HEAT repeat / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Tetratricopeptide repeat / Sec63 Brl domain / : / Leucine-rich repeat / Pre-mRNA-splicing factor Syf1-like / LIS1 homology (LisH) motif profile. / LIS1 homology motif / 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
Similarity search - Domain/homology
: / : / : / 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 ...: / : / : / 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' / Small nuclear ribonucleoprotein-associated proteins B and B' / Microfibrillar-associated protein 1 / NHP2-like protein 1 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / 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 / Protein Red / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / 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 / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm2 / 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: 4.5 Å
AuthorsBertram, K. / Kastner, B.
Funding support Germany, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research FoundationSFB 860 Germany
German Research FoundationLU294/15-1 Germany
CitationJournal: Cell / Year: 2017
Title: Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation.
Authors: Karl Bertram / Dmitry E Agafonov / Olexandr Dybkov / David Haselbach / Majety N Leelaram / Cindy L Will / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark /
Abstract: Little is known about the spliceosome's structure before its extensive remodeling into a catalytically active complex. Here, we report a 3D cryo-EM structure of a pre-catalytic human spliceosomal B ...Little is known about the spliceosome's structure before its extensive remodeling into a catalytically active complex. Here, we report a 3D cryo-EM structure of a pre-catalytic human spliceosomal B complex. The U2 snRNP-containing head domain is connected to the B complex main body via three main bridges. U4/U6.U5 tri-snRNP proteins, which are located in the main body, undergo significant rearrangements during tri-snRNP integration into the B complex. These include formation of a partially closed Prp8 conformation that creates, together with Dim1, a 5' splice site (ss) binding pocket, displacement of Sad1, and rearrangement of Brr2 such that it contacts its U4/U6 substrate and is poised for the subsequent spliceosome activation step. The molecular organization of several B-specific proteins suggests that they are involved in negatively regulating Brr2, positioning the U6/5'ss helix, and stabilizing the B complex structure. Our results indicate significant differences between the early activation phase of human and yeast spliceosomes.
History
DepositionJun 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn

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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: U5 small nuclear ribonucleoprotein 200 kDa helicase
D: U5 small nuclear ribonucleoprotein 40 kDa protein
E: U4/U6 small nuclear ribonucleoprotein Prp3
F: U4/U6 small nuclear ribonucleoprotein Prp4
G: Pre-mRNA-processing factor 6
H: U4/U6 small nuclear ribonucleoprotein Prp31
I: Pre-mRNA-splicing factor 38A
J: Thioredoxin-like protein 4A
K: Microfibrillar-associated protein 1
L: WD40 repeat-containing protein SMU1
M: Peptidyl-prolyl cis-trans isomerase H
N: Zinc finger matrin-type protein 2
O: NHP2-like protein 1
P: U4/U6.U5 tri-snRNP-associated protein 1
Q: WW domain-binding protein 4
R: Protein Red
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: U6 snRNA-associated Sm-like protein LSm2
p: U6 snRNA-associated Sm-like protein LSm3
q: U6 snRNA-associated Sm-like protein LSm4
r: U6 snRNA-associated Sm-like protein LSm5
s: U6 snRNA-associated Sm-like protein LSm6
t: U6 snRNA-associated Sm-like protein LSm7
u: U6 snRNA-associated Sm-like protein LSm8
v: Splicing factor 3B subunit 1
w: Splicing factor 3B subunit 3 (SF3B3)
x: Splicing factor 3B subunit 5
y: PHD finger-like domain-containing protein 5A
z: U2 small nuclear ribonucleoprotein A'
1: U2 small nuclear ribonucleoprotein B''
S: Small nuclear ribonucleoprotein Sm D2
T: Small nuclear ribonucleoprotein F
U: Small nuclear ribonucleoprotein E
V: Small nuclear ribonucleoprotein G
W: Small nuclear ribonucleoprotein Sm D3
X: Small nuclear ribonucleoprotein-associated proteins B and B'
Z: Small nuclear ribonucleoprotein Sm D1
Y: MINX pre-mRNA
2: Human gene for small nuclear RNA U2 (snRNA U2)
4: Homo sapiens U4A snRNA
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)2,389,15057
Polymers2,389,15057
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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Protein , 15 types, 17 molecules ABGIJKLMNOPQRfmXy

#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
#7: 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 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
#10: 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
#11: Protein Microfibrillar-associated protein 1


Mass: 52050.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55081
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: Protein Protein Red / Cytokine IK / IK factor / Protein RER


Mass: 65731.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13123
#24: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B' / Coordinate model: Cα atoms only (Chain-X)


Mass: 24642.131 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#36: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b / Coordinate model: Cα atoms only


Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0

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

#3: 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
#4: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein ...U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57 / Coordinate model: Cα atoms only


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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U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules EFH

#5: 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
#6: Protein U4/U6 small nuclear ribonucleoprotein Prp4 / PRP4 homolog / hPrp4 / U4/U6 snRNP 60 kDa protein / WD splicing factor Prp4


Mass: 58407.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43172
#8: 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

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Small nuclear ribonucleoprotein ... , 6 types, 18 molecules ahSbiTcjUdkVelWgnZ

#19: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2 / Coordinate model: Cα atoms only (Chain-S)


Mass: 13551.928 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#20: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF / Coordinate model: Cα atoms only (Chain-T)


Mass: 9734.171 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#21: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE / Coordinate model: Cα atoms only (Chain-U)


Mass: 10817.601 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#22: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG / Coordinate model: Cα atoms only (Chain-V)


Mass: 8508.084 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308
#23: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3 / Coordinate model: Cα atoms only (Chain-W)


Mass: 13940.308 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#25: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1 / Coordinate model: Cα atoms only (Chain-Z)


Mass: 13310.653 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314

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

#26: Protein U6 snRNA-associated Sm-like protein LSm2 / Protein G7b / Small nuclear ribonuclear protein D homolog / snRNP core Sm-like protein Sm-x5 / Coordinate model: Cα atoms only


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


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


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


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


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


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


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 ... , 3 types, 3 molecules vwx

#33: Protein Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155 / Coordinate model: Cα atoms only


Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533
#34: Protein Splicing factor 3B subunit 3 (SF3B3) / Coordinate model: Cα atoms only


Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393
#35: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit / Coordinate model: Cα atoms only


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 z1

#37: Protein U2 small nuclear ribonucleoprotein A' / U2 snRNP A' / Coordinate model: Cα atoms only


Mass: 28631.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09661
#38: Protein U2 small nuclear ribonucleoprotein B'' / U2 snRNP B'' / Coordinate model: Cα atoms only


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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RNA chain , 2 types, 2 molecules Y2

#39: RNA chain MINX pre-mRNA


Mass: 103979.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#40: 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 ... , 3 types, 3 molecules 456

#41: RNA chain Homo sapiens U4A snRNA


Mass: 46528.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36174
#42: 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
#43: 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 B Complex Spliceosome, sharpened map, masked refinement
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
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 / 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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.05 sec. / Electron dose: 1.5 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 17 / Used frames/image: 2-17

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Processing

Image processingDetails: FALCON III Direct Electron Detector
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44629 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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