3JB9

Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structure of a yeast spliceosome at 3.6-angstrom resolution

Yan, C.Hang, J.Wan, R.Huang, M.Wong, C.Shi, Y.

(2015) Science 349: 1182-1191

  • DOI: 10.1126/science.aac7629
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofac ...

    Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mRNA splicing.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor spp42
A
2363Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: spp42cwf6SPAC4F8.12c
Find proteins for O14187 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf10
B
984Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf10snu114spef2SPBC215.12
Find proteins for O94316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94316

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
D, Z
97Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smd3SPBC19C2.14
Find proteins for Q9UUC6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9UUC6

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
E, b
147Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smb1SPAC26A3.08
Find proteins for Q10163 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10163

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
F, f
117Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smd1SPAC27D7.07c
Find proteins for O42661 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
G, l
115Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smd2cwf9SPAC2C4.03c
Find proteins for O14036 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
H, m
84Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: sme1SPBC11G11.06c
Find proteins for Q9USZ3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
I, n
78Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smf1SPBC3E7.14SPBC4F6.01
Find proteins for O59734 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
J, o
77Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smg1SPBC4B4.05
Find proteins for O74966 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor prp5
K
473Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp5cwf1pi024SPBP22H7.07
Find proteins for O13615 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf17
L
340Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf17SPBC1289.11
Find proteins for O94620 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing protein 45
M
557Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp45cwf13snw1SPCC188.11SPCC584.08
Find proteins for Q09882 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
S, T, U, V
488Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp19cwf8SPAC29A4.08c
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for O14011 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cdc5
W
757Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cdc5SPAC644.12
Find proteins for P39964 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf2
Y
388Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf2prp3SPAC3A12.11c
Find proteins for P87126 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf5
a
354Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf5ecm2SPCC550.02c
Find proteins for O59800 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O59800

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf19
c
639Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf19SPAC30D11.09
Find proteins for Q09909 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q09909

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase ppi1
d
155Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ppi1cyp2SPAC57A10.03
EC: 5.2.1.8
Find proteins for P87051 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf14
e
146Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf14SPBC24C6.11
Find proteins for O74772 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
g
558Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp17SPBC6B1.10
Find proteins for O43071 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf15
h
265Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf15SPBC337.06c
Find proteins for P78794 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf7
i
187Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf7spf27SPBC28F2.04c
Find proteins for Q9USV3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf4
R
674Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf4syf3SPBC31F10.11c
Find proteins for P87312 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf3
r
790Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf3syf1SPBC211.02c
Find proteins for Q9P7R9 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9P7R9

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf11
X
1284Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf11SPBC646.02
Find proteins for O94508 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
j
239Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lea1SPBC1861.08c
Find proteins for Q9USX8 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9USX8

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Probable U2 small nuclear ribonucleoprotein B''
k
111Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: msl1pi056SPBC8D2.09c
Find proteins for Q7LL14 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q7LL14

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
unknown chain
x
412Schizosaccharomyces pombe 972h-Mutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 3
MoleculeChainsLengthOrganism
U5 snRNAC120Schizosaccharomyces pombe

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Entity ID: 14
MoleculeChainsLengthOrganism
U6 snRNAN99Schizosaccharomyces pombe
Entity ID: 15
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3')O8Schizosaccharomyces pombe
Entity ID: 16
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*C)-3')Q13Schizosaccharomyces pombe

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Entity ID: 17
MoleculeChainsLengthOrganism
U2 snRNAP186Schizosaccharomyces pombe
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ADP
Query on ADP

Download CCD File 
X
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

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Y, a, c, e
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 2.0: 2019-12-11
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other