6QDV

Human post-catalytic P complex spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation.

Fica, S.M.Oubridge, C.Wilkinson, M.E.Newman, A.J.Nagai, K.

(2019) Science 363: 710-714

  • DOI: 10.1126/science.aaw5569
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • During exon ligation, the Saccharomyces cerevisiae spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized b ...

    During exon ligation, the Saccharomyces cerevisiae spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8. Here we present the 3.3-angstrom cryo-electron microscopy structure of a human postcatalytic spliceosome just after exon ligation. The 3'SS docks at the active site through conserved RNA interactions in the absence of Prp18. Unexpectedly, the metazoan-specific FAM32A directly bridges the 5'-exon and intron 3'SS of pre-mRNA and promotes exon ligation, as shown by functional assays. CACTIN, SDE2, and NKAP-factors implicated in alternative splicing-further stabilize the catalytic conformation of the spliceosome during exon ligation. Together these four proteins act as exon ligation factors. Our study reveals how the human spliceosome has co-opted additional proteins to modulate a conserved RNA-based mechanism for 3'SS selection and to potentially fine-tune alternative splicing at the exon ligation stage.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. sfica@mrc-lmb.cam.ac.uk kn@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic initiation factor 4A-III
7
390Homo sapiensMutation(s): 0 
Gene Names: EIF4A3DDX48KIAA0111
EC: 3.6.4.13
Find proteins for P38919 (Homo sapiens)
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PHAROS  P38919
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein 8A
8
91Homo sapiensMutation(s): 0 
Gene Names: RBM8ARBM8HSPC114MDS014
Find proteins for Q9Y5S9 (Homo sapiens)
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PHAROS  Q9Y5S9
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 200 kDa helicase
B
1722Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
Find proteins for O75643 (Homo sapiens)
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PHAROS  O75643
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Protein FAM32A
G
60Homo sapiensMutation(s): 0 
Gene Names: FAM32AOTAG12CGI-144
Find proteins for Q9Y421 (Homo sapiens)
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PHAROS  Q9Y421
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22 homolog
H
908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
Find proteins for Q9HCG8 (Homo sapiens)
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PHAROS  Q9HCG8
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Pleiotropic regulator 1
J
320Homo sapiensMutation(s): 0 
Gene Names: PLRG1
Find proteins for O43660 (Homo sapiens)
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PHAROS  O43660
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Protein BUD31 homolog
L
144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
Find proteins for P41223 (Homo sapiens)
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PHAROS  P41223
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 40 kDa protein
N
306Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
Find proteins for Q96DI7 (Homo sapiens)
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PHAROS  Q96DI7
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Spliceosome-associated protein CWC15 homolog
P
229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
Find proteins for Q9P013 (Homo sapiens)
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PHAROS  Q9P013
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Crooked neck-like protein 1
S
848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
Find proteins for Q9BZJ0 (Homo sapiens)
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PHAROS  Q9BZJ0
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Intron-binding protein aquarius
U
1485Homo sapiensMutation(s): 0 
Gene Names: AQRKIAA0560
EC: 3.6.4.13
Find proteins for O60306 (Homo sapiens)
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PHAROS  O60306
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase DHX8
V
1220Homo sapiensMutation(s): 0 
Gene Names: DHX8DDX8
EC: 3.6.4.13
Find proteins for Q14562 (Homo sapiens)
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PHAROS  Q14562
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'
b, k
82Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
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PHAROS  P14678
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e, p
81Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
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PHAROS  P62304
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g, r
73Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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PHAROS  P62308
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
h, l
80Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
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PHAROS  P62314
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
j, m
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
Find proteins for P62316 (Homo sapiens)
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PHAROS  P62316
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
t, u, v, w
504Homo sapiensMutation(s): 0 
Gene Names: PRPF19NMP200PRP19SNEV
EC: 2.3.2.27
Find proteins for Q9UMS4 (Homo sapiens)
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PHAROS  Q9UMS4
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF2
y
144Homo sapiensMutation(s): 0 
Gene Names: SYF2CBPINGCIPIP
Find proteins for O95926 (Homo sapiens)
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PHAROS  O95926
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PRKR-interacting protein 1
D
123Homo sapiensMutation(s): 0 
Gene Names: PRKRIP1
Find proteins for Q9H875 (Homo sapiens)
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PHAROS  Q9H875
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Cactin
F
122Homo sapiensMutation(s): 0 
Gene Names: CACTINC19orf29
Find proteins for Q8WUQ7 (Homo sapiens)
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PHAROS  Q8WUQ7
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
SNW domain-containing protein 1
K
295Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
Find proteins for Q13573 (Homo sapiens)
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PHAROS  Q13573
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RBM22
M
289Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
Find proteins for Q9NW64 (Homo sapiens)
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PHAROS  Q9NW64
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Cell division cycle 5-like protein
O
802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
Find proteins for Q99459 (Homo sapiens)
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PHAROS  Q99459
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Serine/arginine repetitive matrix protein 2
R
26Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
Find proteins for Q9UQ35 (Homo sapiens)
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PHAROS  Q9UQ35
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
T
855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
Find proteins for Q9HCS7 (Homo sapiens)
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PHAROS  Q9HCS7
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
W
162Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
Find proteins for P09661 (Homo sapiens)
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PHAROS  P09661
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
Y
92Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
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PHAROS  P08579
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
NF-kappa-B-activating protein
Z
30Homo sapiensMutation(s): 0 
Gene Names: NKAP
Find proteins for Q8N5F7 (Homo sapiens)
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PHAROS  Q8N5F7
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLU7
c
586Homo sapiensMutation(s): 0 
Gene Names: SLU7
Find proteins for O95391 (Homo sapiens)
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PHAROS  O95391
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
d, n
84Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to UniProtKB:  P62318
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PHAROS  P62318
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f, q
72Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
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PHAROS  P62306
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase-like 1
i
164Homo sapiensMutation(s): 0 
Gene Names: PPIL1CYPL1CGI-124UNQ2425/PRO4984
EC: 5.2.1.8
Find proteins for Q9Y3C6 (Homo sapiens)
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PHAROS  Q9Y3C6
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
o
513Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
Find proteins for O60508 (Homo sapiens)
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PHAROS  O60508
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SPF27
s
225Homo sapiensMutation(s): 0 
Gene Names: BCAS2DAM1
Find proteins for O75934 (Homo sapiens)
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PHAROS  O75934
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Replication stress response regulator SDE2
z
34Homo sapiensMutation(s): 0 
Gene Names: SDE2C1orf55
Find proteins for Q6IQ49 (Homo sapiens)
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PHAROS  Q6IQ49
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Protein mago nashi homolog 2
9
144Homo sapiensMutation(s): 0 
Gene Names: MAGOHBMAGOH2
Find proteins for Q96A72 (Homo sapiens)
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PHAROS  Q96A72
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing-splicing factor 8
A
2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
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PHAROS  Q6P2Q9
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
116 kDa U5 small nuclear ribonucleoprotein component
C
899Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
Find proteins for Q15029 (Homo sapiens)
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PHAROS  Q15029
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Entity ID: 1
MoleculeChainsLengthOrganism
U2 snRNA2189Homo sapiens

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Entity ID: 2
MoleculeChainsLengthOrganism
U5 snRNA5116Homo sapiens
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Entity ID: 11
MoleculeChainsLengthOrganism
Ligated exons: MINX mRNAE14Human adenovirus 2

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Entity ID: 15
MoleculeChainsLengthOrganism
Intron lariat: MINX RNAI113Human adenovirus 2

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Entity ID: 3
MoleculeChainsLengthOrganism
U6 snRNA6106Homo sapiens
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I6P
Query on I6P

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c
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP
Query on GTP

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C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ATP
Query on ATP

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7
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

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L, M, c
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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6
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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6, 7, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
KL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184330
European Research CouncilAdG-693087-SPLICE3D

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references