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: 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 ...

    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

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8A2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentC972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseD2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinE357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3F [auth a],
P [auth h]
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'G [auth b],
Q [auth i]
240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1H [auth c],
R [auth j]
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2I [auth d],
S [auth k]
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FJ [auth f],
T [auth m]
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EK [auth e],
U [auth l]
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GL [auth g],
V [auth n]
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel modifier 1W [auth v]230Homo sapiensMutation(s): 0 
Gene Names: SCNM1
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1X [auth 1]1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2Y [auth 2]895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3Z [auth 3]1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4AA [auth 4]424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6BA [auth 5]125Homo sapiensMutation(s): 0 
Gene Names: SF3B6SAP14SF3B14SF3B14ACGI-110HSPC175HT006
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5ACA [auth 6]110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5DA [auth 7]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinEA [auth L]802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1FA [auth J]848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologGA [auth P]229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1HA [auth R]536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1IA [auth T]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 29
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Smad nuclear-interacting protein 1JA [auth X]396Homo sapiensMutation(s): 0 
Gene Names: SNIP1
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2KA [auth Y]322Homo sapiensMutation(s): 0 
Gene Names: RBMX2CGI-79
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
BUD13 homologLA [auth Z]619Homo sapiensMutation(s): 0 
Gene Names: BUD13
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
RING-type E3 ubiquitin-protein ligase PPIL2MA [auth 9]520Homo sapiensMutation(s): 0 
Gene Names: PPIL2
EC: 2.3.2.27
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase CWC27 homologNA [auth z]472Homo sapiensMutation(s): 0 
Gene Names: CWC27SDCCAG10UNQ438/PRO871
EC: 5.2.1.8
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16OA [auth x]1041Homo sapiensMutation(s): 0 
Gene Names: DHX16DBP2DDX16KIAA0577PRP2
EC: 3.6.4.13
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
G-patch domain and KOW motifs-containing proteinPA [auth y]476Homo sapiensMutation(s): 0 
Gene Names: GPKOWGPATC5GPATCH5T54
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
RING finger protein 113AQA [auth M]343Homo sapiensMutation(s): 0 
Gene Names: RNF113ARNF113ZNF183
EC: 2.3.2.27
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2RA [auth U]2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
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Entity ID: 38
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Pre-mRNA-splicing factor CWC22 homologSA [auth V]908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
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Entity ID: 39
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Serine/arginine repetitive matrix protein 1TA [auth 8]904Homo sapiensMutation(s): 0 
Gene Names: SRRM1SRM160
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Cysteine-rich PDZ-binding proteinUA [auth 0]101Homo sapiensMutation(s): 0 
Gene Names: CRIPTHSPC139
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein 48VA [auth I]367Homo sapiensMutation(s): 0 
Gene Names: RBM48C7orf64HSPC304
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Armadillo repeat-containing protein 7WA [auth K]198Homo sapiensMutation(s): 0 
Gene Names: ARMC7
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNAB 117Homo sapiens
Protein Feature View
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  • Reference Sequence
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Entity ID: 13
MoleculeChainsLengthOrganismImage
U6atac snRNAM [auth F]124Homo sapiens
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Entity ID: 14
MoleculeChainsLengthOrganismImage
pre-mRNAN [auth G]142Homo sapiens
Protein Feature View
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Entity ID: 15
MoleculeChainsLengthOrganismImage
U12 snRNAO [auth H]150Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

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XA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
K (Subject of Investigation/LOI)
Query on K

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EB [auth F],
FB [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D 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