3JB9

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor spp42
A
2363Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: spp42 (cwf6)
Find proteins for O14187 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14187
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf10
B
984Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf10 (snu114, spef2)
Find proteins for O94316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94316
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
D, Z
97Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: smd3
Find proteins for Q9UUC6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9UUC6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
E, b
147Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: smb1
Find proteins for Q10163 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10163
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
F, f
117Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: smd1
Find proteins for O42661 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O42661
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
G, l
115Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: smd2 (cwf9)
Find proteins for O14036 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14036
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
H, m
84Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: sme1
Find proteins for Q9USZ3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9USZ3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
I, n
78Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: smf1
Find proteins for O59734 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O59734
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
J, o
77Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: smg1
Find proteins for O74966 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74966
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor prp5
K
473Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: prp5 (cwf1)
Find proteins for O13615 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O13615
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf17
L
340Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf17
Find proteins for O94620 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94620
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing protein 45
M
557Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: prp45 (cwf13, snw1)
Find proteins for Q09882 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q09882
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
S, T, U, V
488Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: prp19 (cwf8)
EC: 2.3.2.27
Find proteins for O14011 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14011
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cdc5
W
757Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cdc5
Find proteins for P39964 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P39964
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf2
Y
388Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf2 (prp3)
Find proteins for P87126 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P87126
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf5
a
354Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf5 (ecm2)
Find proteins for O59800 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O59800
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf19
c
639Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf19
Find proteins for Q09909 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q09909
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase ppi1
d
155Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: ppi1 (cyp2)
EC: 5.2.1.8
Find proteins for P87051 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P87051
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf14
e
146Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf14
Find proteins for O74772 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74772
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
g
558Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: prp17
Find proteins for O43071 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O43071
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf15
h
265Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf15
Find proteins for P78794 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P78794
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf7
i
187Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf7 (spf27)
Find proteins for Q9USV3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9USV3
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf4
R
674Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf4 (syf3)
Find proteins for P87312 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P87312
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf3
r
790Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf3 (syf1)
Find proteins for Q9P7R9 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9P7R9
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor cwf11
X
1284Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cwf11
Find proteins for O94508 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94508
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
j
239Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: lea1
Find proteins for Q9USX8 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9USX8
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Probable U2 small nuclear ribonucleoprotein B''
k
111Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: msl1
Find proteins for Q7LL14 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q7LL14
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
unknown chain
x
412N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsLengthOrganism
U5 snRNAC120Schizosaccharomyces pombe
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
Entity ID: 17
MoleculeChainsLengthOrganism
U2 snRNAP186Schizosaccharomyces pombe
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

Download SDF File 
Download CCD File 
a, c, e, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
a, K, R, r, W, x, Y
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release