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

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8A2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8, PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
Explore Q6P2Q9 
Go to UniProtKB:  Q6P2Q9
NIH Common Fund Data Resources
PHAROS  Q6P2Q9
GTEx  ENSG00000174231
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentC972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2, KIAA0031, SNRP116
Find proteins for Q15029 (Homo sapiens)
Explore Q15029 
Go to UniProtKB:  Q15029
NIH Common Fund Data Resources
PHAROS  Q15029
GTEx  ENSG00000108883
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseD2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200, ASCC3L1, HELIC2, KIAA0788
EC: 3.6.4.13
Find proteins for O75643 (Homo sapiens)
Explore O75643 
Go to UniProtKB:  O75643
NIH Common Fund Data Resources
PHAROS  O75643
GTEx  ENSG00000144028
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinE357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40, PRP8BP, SFP38, WDR57
Find proteins for Q96DI7 (Homo sapiens)
Explore Q96DI7 
Go to UniProtKB:  Q96DI7
NIH Common Fund Data Resources
PHAROS  Q96DI7
GTEx  ENSG00000060688
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3a, h126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Explore P62318 
Go to UniProtKB:  P62318
NIH Common Fund Data Resources
PHAROS  P62318
GTEx  ENSG00000100028
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'b, i231Homo sapiensMutation(s): 0 
Gene Names: SNRPB, COD, SNRPB1
Find proteins for P14678 (Homo sapiens)
Explore P14678 
Go to UniProtKB:  P14678
NIH Common Fund Data Resources
PHAROS  P14678
GTEx  ENSG00000125835
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1c, j119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Explore P62314 
Go to UniProtKB:  P62314
NIH Common Fund Data Resources
PHAROS  P62314
GTEx  ENSG00000167088
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2d, k118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2, SNRPD1
Find proteins for P62316 (Homo sapiens)
Explore P62316 
Go to UniProtKB:  P62316
NIH Common Fund Data Resources
PHAROS  P62316
GTEx  ENSG00000125743
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Ff, m86Homo sapiensMutation(s): 0 
Gene Names: SNRPF, PBSCF
Find proteins for P62306 (Homo sapiens)
Explore P62306 
Go to UniProtKB:  P62306
NIH Common Fund Data Resources
PHAROS  P62306
GTEx  ENSG00000139343
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Ee, l92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Explore P62304 
Go to UniProtKB:  P62304
NIH Common Fund Data Resources
PHAROS  P62304
GTEx  ENSG00000182004
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Gg, n76Homo sapiensMutation(s): 0 
Gene Names: SNRPG, PBSCG
Find proteins for P62308 (Homo sapiens)
Explore P62308 
Go to UniProtKB:  P62308
NIH Common Fund Data Resources
PHAROS  P62308
GTEx  ENSG00000143977
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'o255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
Find proteins for P09661 (Homo sapiens)
Explore P09661 
Go to UniProtKB:  P09661
NIH Common Fund Data Resources
PHAROS  P09661
GTEx  ENSG00000131876
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''p225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
Explore P08579 
Go to UniProtKB:  P08579
NIH Common Fund Data Resources
PHAROS  P08579
GTEx  ENSG00000125870
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3w501Homo sapiensMutation(s): 0 
Gene Names: SF3A3, SAP61
Find proteins for Q12874 (Homo sapiens)
Explore Q12874 
Go to UniProtKB:  Q12874
NIH Common Fund Data Resources
PHAROS  Q12874
GTEx  ENSG00000183431
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1u793Homo sapiensMutation(s): 0 
Gene Names: SF3A1, SAP114
Find proteins for Q15459 (Homo sapiens)
Explore Q15459 
Go to UniProtKB:  Q15459
NIH Common Fund Data Resources
PHAROS  Q15459
GTEx  ENSG00000099995
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2v464Homo sapiensMutation(s): 0 
Gene Names: SF3A2, SAP62
Find proteins for Q15428 (Homo sapiens)
Explore Q15428 
Go to UniProtKB:  Q15428
NIH Common Fund Data Resources
PHAROS  Q15428
GTEx  ENSG00000104897
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 111304Homo sapiensMutation(s): 0 
Gene Names: SF3B1, SAP155
Find proteins for O75533 (Homo sapiens)
Explore O75533 
Go to UniProtKB:  O75533
NIH Common Fund Data Resources
PHAROS  O75533
GTEx  ENSG00000115524
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 22895Homo sapiensMutation(s): 0 
Gene Names: SF3B2, SAP145
Find proteins for Q13435 (Homo sapiens)
Explore Q13435 
Go to UniProtKB:  Q13435
NIH Common Fund Data Resources
PHAROS  Q13435
GTEx  ENSG00000087365
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 331217Homo sapiensMutation(s): 0 
Gene Names: SF3B3, KIAA0017, SAP130
Find proteins for Q15393 (Homo sapiens)
Explore Q15393 
Go to UniProtKB:  Q15393
NIH Common Fund Data Resources
PHAROS  Q15393
GTEx  ENSG00000189091
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 44424Homo sapiensMutation(s): 0 
Gene Names: SF3B4, SAP49
Find proteins for Q15427 (Homo sapiens)
Explore Q15427 
Go to UniProtKB:  Q15427
NIH Common Fund Data Resources
PHAROS  Q15427
GTEx  ENSG00000143368
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 65125Homo sapiensMutation(s): 0 
Gene Names: SF3B6, SAP14, SF3B14, SF3B14A, CGI-110, HSPC175, HT006
Find proteins for Q9Y3B4 (Homo sapiens)
Explore Q9Y3B4 
Go to UniProtKB:  Q9Y3B4
NIH Common Fund Data Resources
PHAROS  Q9Y3B4
GTEx  ENSG00000115128
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5A6110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
Find proteins for Q7RTV0 (Homo sapiens)
Explore Q7RTV0 
Go to UniProtKB:  Q7RTV0
NIH Common Fund Data Resources
PHAROS  Q7RTV0
GTEx  ENSG00000100410
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5786Homo sapiensMutation(s): 0 
Gene Names: SF3B5, SF3B10
Find proteins for Q9BWJ5 (Homo sapiens)
Explore Q9BWJ5 
Go to UniProtKB:  Q9BWJ5
NIH Common Fund Data Resources
PHAROS  Q9BWJ5
GTEx  ENSG00000169976
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1J848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1, CRN, CGI-201, MSTP021
Find proteins for Q9BZJ0 (Homo sapiens)
Explore Q9BZJ0 
Go to UniProtKB:  Q9BZJ0
NIH Common Fund Data Resources
PHAROS  Q9BZJ0
GTEx  ENSG00000101343
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinL802Homo sapiensMutation(s): 0 
Gene Names: CDC5L, KIAA0432, PCDC5RP
Find proteins for Q99459 (Homo sapiens)
Explore Q99459 
Go to UniProtKB:  Q99459
NIH Common Fund Data Resources
PHAROS  Q99459
GTEx  ENSG00000096401
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
RING finger protein 113AM343Homo sapiensMutation(s): 0 
Gene Names: RNF113A, RNF113, ZNF183
EC: 2.3.2.27
Find proteins for O15541 (Homo sapiens)
Explore O15541 
Go to UniProtKB:  O15541
NIH Common Fund Data Resources
PHAROS  O15541
GTEx  ENSG00000125352
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologP229Homo sapiensMutation(s): 0 
Gene Names: CWC15, C11orf5, AD-002, HSPC148
Find proteins for Q9P013 (Homo sapiens)
Explore Q9P013 
Go to UniProtKB:  Q9P013
NIH Common Fund Data Resources
PHAROS  Q9P013
GTEx  ENSG00000150316
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
SkipR540Homo sapiensMutation(s): 0 
Gene Names: SNW1, SKIIP, SKIP
Find proteins for Q13573 (Homo sapiens)
Explore Q13573 
Go to UniProtKB:  Q13573
NIH Common Fund Data Resources
PHAROS  Q13573
GTEx  ENSG00000100603
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1T514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
Find proteins for O43660 (Homo sapiens)
Explore O43660 
Go to UniProtKB:  O43660
NIH Common Fund Data Resources
PHAROS  O43660
GTEx  ENSG00000171566
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologV908Homo sapiensMutation(s): 0 
Gene Names: CWC22, KIAA1604, NCM
Find proteins for Q9HCG8 (Homo sapiens)
Explore Q9HCG8 
Go to UniProtKB:  Q9HCG8
NIH Common Fund Data Resources
PHAROS  Q9HCG8
GTEx  ENSG00000163510
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1X396Homo sapiensMutation(s): 0 
Gene Names: SNIP1
Find proteins for Q8TAD8 (Homo sapiens)
Explore Q8TAD8 
Go to UniProtKB:  Q8TAD8
NIH Common Fund Data Resources
PHAROS  Q8TAD8
GTEx  ENSG00000163877
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2Y322Homo sapiensMutation(s): 0 
Gene Names: RBMX2, CGI-79
Find proteins for Q9Y388 (Homo sapiens)
Explore Q9Y388 
Go to UniProtKB:  Q9Y388
NIH Common Fund Data Resources
PHAROS  Q9Y388
GTEx  ENSG00000134597
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
BUD13 homologZ619Homo sapiensMutation(s): 0 
Gene Names: BUD13
Find proteins for Q9BRD0 (Homo sapiens)
Explore Q9BRD0 
Go to UniProtKB:  Q9BRD0
NIH Common Fund Data Resources
PHAROS  Q9BRD0
GTEx  ENSG00000137656
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase CWC27 homologz472Homo sapiensMutation(s): 0 
Gene Names: CWC27, SDCCAG10, UNQ438/PRO871
EC: 5.2.1.8
Find proteins for Q6UX04 (Homo sapiens)
Explore Q6UX04 
Go to UniProtKB:  Q6UX04
NIH Common Fund Data Resources
PHAROS  Q6UX04
GTEx  ENSG00000153015
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16x1041Homo sapiensMutation(s): 0 
Gene Names: DHX16, DBP2, DDX16, KIAA0577, PRP2
EC: 3.6.4.13
Find proteins for O60231 (Homo sapiens)
Explore O60231 
Go to UniProtKB:  O60231
NIH Common Fund Data Resources
PHAROS  O60231
GTEx  ENSG00000204560
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNAB117Homo sapiens
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsLengthOrganismImage
U6 snRNAF107Homo sapiens
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsLengthOrganismImage
pre-mRNAG274unidentified adenovirus
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
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

View Full Validation Report


View more in-depth experimental data

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