5Z58

Cryo-EM structure of a human activated spliceosome (early Bact) at 4.9 angstrom.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report



Literature

Structure of the human activated spliceosome in three conformational states.

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

(2018) Cell Res 28: 307-322

  • DOI: 10.1038/cr.2018.14
  • Primary Citation of Related Structures:  
    5Z57, 5Z56, 5Z58

  • PubMed Abstract: 
  • During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B act complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we pres ...

    During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B act complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we present the cryo-EM structure of the human B act complex in three distinct conformational states. The EM map allows atomic modeling of nearly all protein components of the U2 small nuclear ribonucleoprotein (snRNP), including three of the SF3a complex and seven of the SF3b complex. The structure of the human B act complex contains 52 proteins, U2, U5, and U6 small nuclear RNA (snRNA), and a pre-mRNA. Three distinct conformations have been captured, representing the early, mature, and late states of the human B act complex. These complexes differ in the orientation of the Switch loop of Prp8, the splicing factors RNF113A and NY-CO-10, and most components of the NineTeen complex (NTC) and the NTC-related complex. Analysis of these three complexes and comparison with the B and C complexes reveal an ordered flux of components in the B-to-B act and the B act -to-B * transitions, which ultimately prime the active site for the branching reaction.


    Organizational Affiliation

    Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Shilongshan Road No. 18, Hangzhou, Zhejiang 310064, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8A2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
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PHAROS  Q6P2Q9
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentC972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
Find proteins for Q15029 (Homo sapiens)
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PHAROS  Q15029
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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
Find proteins for O75643 (Homo sapiens)
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PHAROS  O75643
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinE357Homo 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 LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3ah126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
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PHAROS  P62318
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'bi231Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
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PHAROS  P14678
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1cj119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
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PHAROS  P62314
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2dk118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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PHAROS  P62316
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Ffm86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
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PHAROS  P62306
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Eel92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Ggn76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'o255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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PHAROS  P09661
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''p225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3w501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
Find proteins for Q12874 (Homo sapiens)
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PHAROS  Q12874
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1u793Homo sapiensMutation(s): 0 
Gene Names: SF3A1SAP114
Find proteins for Q15459 (Homo sapiens)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2v464Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
Find proteins for Q15428 (Homo sapiens)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 111304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
Find proteins for O75533 (Homo sapiens)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 22895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
Find proteins for Q13435 (Homo sapiens)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 331217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
Find proteins for Q15393 (Homo sapiens)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 44424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
Find proteins for Q15427 (Homo sapiens)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 65125Homo sapiensMutation(s): 0 
Gene Names: SF3B6SAP14SF3B14SF3B14ACGI-110HSPC175HT006
Find proteins for Q9Y3B4 (Homo sapiens)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5A6110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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PHAROS  Q7RTV0
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5786Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
Find proteins for Q9BWJ5 (Homo sapiens)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1J848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
Find proteins for Q9BZJ0 (Homo sapiens)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinL802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
Find proteins for Q99459 (Homo sapiens)
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PHAROS  Q99459
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
RING finger protein 113AM343Homo sapiensMutation(s): 0 
Gene Names: RNF113ARNF113ZNF183
EC: 2.3.2.27
Find proteins for O15541 (Homo sapiens)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologP229Homo 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: 32
MoleculeChainsSequence LengthOrganismDetailsImage
SkipR540Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
Find proteins for Q13573 (Homo sapiens)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1T514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologV908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
Find proteins for Q9HCG8 (Homo sapiens)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1X396Homo sapiensMutation(s): 0 
Gene Names: SNIP1
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2Y322Homo sapiensMutation(s): 0 
Gene Names: RBMX2CGI-79
Find proteins for Q9Y388 (Homo sapiens)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
BUD13 homologZ619Homo sapiensMutation(s): 0 
Gene Names: BUD13
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase CWC27 homologz472Homo sapiensMutation(s): 0 
Gene Names: CWC27SDCCAG10UNQ438/PRO871
EC: 5.2.1.8
Find proteins for Q6UX04 (Homo sapiens)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16x1041Homo sapiensMutation(s): 0 
Gene Names: DHX16DBP2DDX16KIAA0577PRP2
EC: 3.6.4.13
Find proteins for O60231 (Homo sapiens)
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNAB117Homo sapiens
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Entity ID: 13
MoleculeChainsLengthOrganismImage
U6 snRNAF107Homo sapiens
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Entity ID: 14
MoleculeChainsLengthOrganismImage
pre-mRNAG274unidentified adenovirus
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Entity ID: 15
MoleculeChainsLengthOrganismImage
U2 snRNAH188Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 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
Ministry of Science and Technology (China)China2016YFA0501100

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2020-10-14
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary