7DVQ

Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 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 the activated human minor spliceosome.

Bai, R.Wan, R.Wang, L.Xu, K.Zhang, Q.Lei, J.Shi, Y.

(2021) Science 371

  • DOI: https://doi.org/10.1126/science.abg0879
  • Primary Citation of Related Structures:  
    7DVQ

  • PubMed Abstract: 

    The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo-electron microscopy at 2.9-angstrom resolution. The 5' splice site and branch point sequence of the U12-type intron are recognized by the U6atac and U12 small nuclear RNAs (snRNAs), respectively. Five newly identified proteins stabilize the conformation of the catalytic center: The zinc finger protein SCNM1 functionally mimics the SF3a complex of the major spliceosome, the RBM48-ARMC7 complex binds the γ-monomethyl phosphate cap at the 5' end of U6atac snRNA, the U-box protein PPIL2 coordinates loop I of U5 snRNA and stabilizes U5 small nuclear ribonucleoprotein (snRNP), and CRIPT stabilizes U12 snRNP. Our study provides a framework for the mechanistic understanding of the function of the human minor spliceosome.


  • Organizational Affiliation

    Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3F [auth a],
P [auth h]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'G [auth b],
Q [auth i]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1H [auth c],
R [auth j]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2I [auth d],
S [auth k]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FJ [auth f],
T [auth m]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EK [auth e],
U [auth l]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GL [auth g],
V [auth n]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel modifier 1W [auth v]230Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163156 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1X [auth 1]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2Y [auth 2]895Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087365 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3Z [auth 3]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4AA [auth 4]424Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143368 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6BA [auth 5]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115128 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5ACA [auth 6]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5DA [auth 7]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169976 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinEA [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1FA [auth J]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologGA [auth P]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1HA [auth R]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1IA [auth T]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1JA [auth X]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163877 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2KA [auth Y]322Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134597 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
BUD13 homologLA [auth Z]619Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137656 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RING-type E3 ubiquitin-protein ligase PPIL2MA [auth 9]520Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000100023 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase CWC27 homologNA [auth z]472Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000153015 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16OA [auth x]1,041Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000204560 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
G-patch domain and KOW motifs-containing proteinPA [auth y]476Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000068394 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
RING finger protein 113AQA [auth M]343Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125352 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2RA [auth U]2,752Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167978 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologSA [auth V]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 1TA [auth 8]904Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000133226 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine-rich PDZ-binding proteinUA [auth 0]101Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000119878 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 48VA [auth I]367Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127993 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Armadillo repeat-containing protein 7WA [auth K]198Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125449 
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNA117Homo sapiens
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Entity ID: 13
MoleculeChains LengthOrganismImage
U6atac snRNAM [auth F]124Homo sapiens
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Entity ID: 14
MoleculeChains LengthOrganismImage
pre-mRNAN [auth G]142Homo sapiens
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains LengthOrganismImage
U12 snRNAO [auth H]150Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
XA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
G5J (Subject of Investigation/LOI)
Query on G5J

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GB [auth F]5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine
C11 H18 N5 O14 P3
DJZJYVFASQUZKQ-KQYNXXCUSA-N
GTP (Subject of Investigation/LOI)
Query on GTP

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YA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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HB [auth v]
IB [auth 6]
JB [auth 6]
KB [auth 6]
LB [auth M]
HB [auth v],
IB [auth 6],
JB [auth 6],
KB [auth 6],
LB [auth M],
MB [auth 0],
NB [auth 0]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K (Subject of Investigation/LOI)
Query on K

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EB [auth F],
FB [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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AB [auth F],
BB [auth F],
CB [auth F],
DB [auth F],
ZA [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
X [auth 1]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
Z [auth 3]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 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 China (NSFC)China31930059

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release