5XJC

Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

An Atomic Structure of the Human Spliceosome

Zhang, X.Yan, C.Hang, J.Finci, L.I.Lei, J.Shi, Y.

(2017) Cell 169: 918-929.e14

  • DOI: https://doi.org/10.1016/j.cell.2017.04.033
  • Primary Citation of Related Structures:  
    5XJC

  • PubMed Abstract: 

    Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the human spliceosome just before exon ligation (the C complex) at an average resolution of 3.76 Å. The splicing factor Prp17 stabilizes the active site conformation. The step II factor Slu7 adopts an extended conformation, binds Prp8 and Cwc22, and is poised for selection of the 3'-splice site. Remarkably, the intron lariat traverses through a positively charged central channel of RBM22; this unusual organization suggests mechanisms of intron recruitment, confinement, and release. The protein PRKRIP1 forms a 100-Å α helix linking the distant U2 snRNP to the catalytic center. A 35-residue fragment of the ATPase/helicase Prp22 latches onto Prp8, and the quaternary exon junction complex (EJC) recognizes upstream 5'-exon sequences and associates with Cwc22 and the GTPase Snu114. These structural features reveal important mechanistic insights into exon ligation.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 82,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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UniProt GroupQ6P2Q9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein component972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicase2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa protein357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116752 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like protein802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2243Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117614 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homolog144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homolog229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquarius1,485Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000021776 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000137168 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 22,752Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167978 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homolog908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
PRKR-interacting protein 1184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128563 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX81,220Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000067596 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7586Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164609 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3AA [auth a],
HA [auth h]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'BA [auth b],
IA [auth i]
231Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1CA [auth c],
JA [auth j]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2DA [auth d],
KA [auth k]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FEA [auth f],
LA [auth m]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EFA [auth e],
MA [auth l]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GGA [auth g],
NA [auth n]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'OA [auth o]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''PA [auth p]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19QA [auth q],
RA [auth r],
SA [auth s],
TA [auth t]
504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000110107 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIIUA [auth u]411Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000141543 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Protein mago nashi homolog 2VA [auth v]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111196 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 8AWA [auth w]174Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265241 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Protein CASC3XA [auth x]703Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108349 
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNA117Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
U6 snRNA107Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
pre-mRNA275Human adenovirus 2
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Entity ID: 8
MoleculeChains LengthOrganismImage
Homo sapiens small nuclear RNA (U2) gene188Homo sapiens
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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YA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP

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ZA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP
Query on ATP

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QB [auth Q],
VB [auth u]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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BB [auth D],
CB [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

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KB [auth N]
LB [auth N]
MB [auth N]
NB [auth O]
OB [auth O]
KB [auth N],
LB [auth N],
MB [auth N],
NB [auth O],
OB [auth O],
PB [auth O],
TB [auth Z]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth C]
DB [auth D]
EB [auth F]
FB [auth F]
GB [auth F]
AB [auth C],
DB [auth D],
EB [auth F],
FB [auth F],
GB [auth F],
HB [auth F],
IB [auth F],
JB [auth F],
RB [auth Q],
SB [auth Q],
UB [auth u]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
R
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyChina2014ZX09507003006
Ministry of Science and TechnologyChina2016YFA0501100

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Other, Structure summary
  • Version 1.2: 2019-12-04
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2020-10-14
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary