6ID0

Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 complex) at 2.9 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

Structures of the human spliceosomes before and after release of the ligated exon.

Zhang, X.Zhan, X.Yan, C.Zhang, W.Liu, D.Lei, J.Shi, Y.

(2019) Cell Res 29: 274-285

  • DOI: 10.1038/s41422-019-0143-x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this stu ...

    Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this study, we report the cryo-electron microscopy structures of the human post-catalytic spliceosome (P complex) and intron lariat spliceosome (ILS) at average resolutions of 3.0 and 2.9 Å, respectively. In the P complex, the ligated exon remains anchored to loop I of U5 small nuclear RNA, and the 3'-splice site is recognized by the junction between the 5'-splice site and the branch point sequence. The ATPase/helicase Prp22, along with the ligated exon and eight other proteins, are dissociated in the P-to-ILS transition. Intriguingly, the ILS complex exists in two distinct conformations, one with the ATPase/helicase Prp43 and one without. Comparison of these three late-stage human spliceosomes reveals mechanistic insights into exon release and spliceosome disassembly.


    Organizational Affiliation

    School of Life Sciences, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang, 310024, China. shi-lab@tsinghua.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing-splicing factor 8
A
2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
Go to UniProtKB:  Q6P2Q9
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PHAROS  Q6P2Q9

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RBM22
O
420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
Find proteins for Q9NW64 (Homo sapiens)
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PHAROS  Q9NW64

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Entity ID: 11
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: 12
MoleculeChainsSequence LengthOrganismDetails
SNW domain-containing protein 1
R
536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
Find proteins for Q13573 (Homo sapiens)
Go to UniProtKB:  Q13573
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PHAROS  Q13573

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase-like 1
S
166Homo 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: 14
MoleculeChainsSequence LengthOrganismDetails
Pleiotropic regulator 1
T
514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
Find proteins for O43660 (Homo sapiens)
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PHAROS  O43660

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
W
579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
Find proteins for O60508 (Homo sapiens)
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PHAROS  O60508

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
CWF19-like protein 2
U
894Homo sapiensMutation(s): 0 
Gene Names: CWF19L2
Find proteins for Q2TBE0 (Homo sapiens)
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PHAROS  Q2TBE0

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
I
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: 20
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
a, h
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
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PHAROS  P62318

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein
b, i
231Homo sapiensMutation(s): 0 
Gene Names: SNRPBhCG_2039421
Find proteins for Q66K91 (Homo sapiens)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
c, j
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
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PHAROS  P62314

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
d, k
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: 24
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f, m
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
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PHAROS  P62306

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e, l
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
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PHAROS  P62304

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g, n
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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PHAROS  P62308

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
q, r, s, t
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: 28
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SPF27
K
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: 29
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
o
255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
Find proteins for P09661 (Homo sapiens)
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PHAROS  P09661

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
116 kDa U5 small nuclear ribonucleoprotein component
C
972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
Find proteins for Q15029 (Homo sapiens)
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PHAROS  Q15029

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
p
225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
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PHAROS  P08579

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RNA helicase aquarius
Q
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: 32
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase E
y
301Homo sapiensMutation(s): 0 
Gene Names: PPIECYP33
EC: 5.2.1.8
Find proteins for Q9UNP9 (Homo sapiens)
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PHAROS  Q9UNP9

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 40 kDa protein
E
357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
Find proteins for Q96DI7 (Homo sapiens)
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PHAROS  Q96DI7

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Crooked neck-like protein 1
J
848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
Find proteins for Q9BZJ0 (Homo sapiens)
Go to UniProtKB:  Q9BZJ0
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PHAROS  Q9BZJ0

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cell division cycle 5-like protein
L
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: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF2
M
243Homo sapiensMutation(s): 0 
Gene Names: SYF2CBPINGCIPIP
Find proteins for O95926 (Homo sapiens)
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PHAROS  O95926

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Protein BUD31 homolog
N
144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
Find proteins for P41223 (Homo sapiens)
Go to UniProtKB:  P41223
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PHAROS  P41223

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Entity ID: 16
MoleculeChainsLengthOrganism
pre-mRNAG272Homo sapiens

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Entity ID: 17
MoleculeChainsLengthOrganism
U2snRNAH188Homo sapiens

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Entity ID: 2
MoleculeChainsLengthOrganism
U5snRNAB117Homo sapiens

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Entity ID: 5
MoleculeChainsLengthOrganism
U6snRNAF107Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I6P
Query on I6P

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

Download CCD File 
C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
N, O, U
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
C, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
R
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31430020

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references