6AH0

The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the human pre-catalytic spliceosome and its precursor spliceosome.

Zhan, X.Yan, C.Zhang, X.Lei, J.Shi, Y.

(2018) Cell Res 28: 1129-1140

  • DOI: 10.1038/s41422-018-0094-7
  • Primary Citation of Related Structures:  
    6AH0, 6AHD

  • PubMed Abstract: 
  • The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B act complex). The pre-B-to-B and B-to-B act transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively ...

    The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B act complex). The pre-B-to-B and B-to-B act transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5'-exon is anchored to loop I of U5 snRNA, and the 5'-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human spliceosome.


    Organizational Affiliation

    Institute of Biology, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang, 310024, China. shi-lab@tsinghua.edu.cn.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseB [auth D]2,136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinC [auth E]357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2VA [auth P],
D [auth a],
Z [auth k]
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FWA [auth Q],
E [auth b],
AA [auth m]
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EXA [auth R],
F [auth c],
BA [auth l]
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GYA [auth S],
G [auth d],
CA [auth n]
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3ZA [auth T],
H [auth e],
W [auth h]
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'AB [auth U],
I [auth f],
X [auth i]
231Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1BB [auth V],
J [auth g],
Y [auth j]
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2L [auth q]95Homo sapiensMutation(s): 0 
Gene Names: LSM2C6orf28G7B
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Entity ID: 13
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U6 snRNA-associated Sm-like protein LSm3M [auth r]102Homo sapiensMutation(s): 0 
Gene Names: LSM3MDS017
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Entity ID: 14
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U6 snRNA-associated Sm-like protein LSm4N [auth s]139Homo sapiensMutation(s): 0 
Gene Names: LSM4
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Entity ID: 15
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U6 snRNA-associated Sm-like protein LSm5O [auth t]91Homo sapiensMutation(s): 0 
Gene Names: LSM5
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Entity ID: 16
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U6 snRNA-associated Sm-like protein LSm6P [auth x]80Homo sapiensMutation(s): 0 
Gene Names: LSM6
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Entity ID: 17
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U6 snRNA-associated Sm-like protein LSm7Q [auth y]103Homo sapiensMutation(s): 0 
Gene Names: LSM7
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Entity ID: 18
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U6 snRNA-associated Sm-like protein LSm8R [auth z]96Homo sapiensMutation(s): 0 
Gene Names: LSM8
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'U [auth o]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 22
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U2 small nuclear ribonucleoprotein B''V [auth p]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1DA [auth u]793Homo sapiensMutation(s): 0 
Gene Names: SF3A1SAP114
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Entity ID: 24
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Splicing factor 3A subunit 2EA [auth v]464Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3FA [auth w]501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1GA [auth 1]1,304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
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Entity ID: 27
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Splicing factor 3B subunit 2HA [auth 2]895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
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Entity ID: 28
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Splicing factor 3B subunit 3IA [auth 3]1,217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
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Entity ID: 29
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Splicing factor 3B subunit 4JA [auth 4]424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
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Entity ID: 30
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Splicing factor 3B subunit 6KA [auth 5]125Homo sapiensMutation(s): 0 
Gene Names: SF3B6SAP14SF3B14SF3B14ACGI-110HSPC175HT006
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Entity ID: 31
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PHD finger-like domain-containing protein 5ALA [auth 6]110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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Entity ID: 32
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Splicing factor 3B subunit 5MA [auth 7]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Entity ID: 33
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U4/U6 small nuclear ribonucleoprotein Prp3NA [auth J]683Homo sapiensMutation(s): 0 
Gene Names: PRPF3HPRP3PRP3
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Entity ID: 34
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U4/U6 small nuclear ribonucleoprotein Prp4OA [auth K]522Homo sapiensMutation(s): 0 
Gene Names: PRPF4PRP4
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Entity ID: 35
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Pre-mRNA-processing factor 6PA [auth N]941Homo sapiensMutation(s): 0 
Gene Names: PRPF6C20orf14
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Entity ID: 36
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U4/U6 small nuclear ribonucleoprotein Prp31QA [auth L]499Homo sapiensMutation(s): 0 
Gene Names: PRPF31PRP31
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Entity ID: 37
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NHP2-like protein 1RA [auth M]128Homo sapiensMutation(s): 0 
Gene Names: SNU13NHP2L1
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Entity ID: 38
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Thioredoxin-like protein 4ASA [auth O]142Homo sapiensMutation(s): 0 
Gene Names: TXNL4ADIM1TXNL4
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Entity ID: 39
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U4/U6.U5 tri-snRNP-associated protein 2TA [auth W]565Homo sapiensMutation(s): 0 
Gene Names: USP39CGI-21HSPC332PRO2855
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX23CB [auth X]820Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
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Entity ID: 42
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Pre-mRNA-processing-splicing factor 8DB [auth A]2,335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Entity ID: 43
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116 kDa U5 small nuclear ribonucleoprotein componentEB [auth C]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Go to UniProtKB:  Q15029
PHAROS:  Q15029
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15029
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U5snRNAA [auth B]117Homo sapiens
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Entity ID: 11
MoleculeChainsLengthOrganismImage
U6snRNAK [auth F]107Homo sapiens
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Entity ID: 19
MoleculeChainsLengthOrganismImage
pre-mRNAS [auth G]274Homo sapiens
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Entity ID: 20
MoleculeChainsLengthOrganismImage
U2snRNAT [auth H]188Homo sapiens
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Entity ID: 40
MoleculeChainsLengthOrganismImage
U4snRNAUA [auth I]144Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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

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GB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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HB [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2020-10-14
    Changes: Structure summary