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


This is version 2.0 of the entry. See complete history


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: https://doi.org/10.1038/cr.2018.14
  • Primary Citation of Related Structures:  
    5Z56, 5Z57, 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 82,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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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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PHAROS:  Q96DI7
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]
231Homo 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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PHAROS:  P62306
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
U2 small nuclear ribonucleoprotein A'W [auth o]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''X [auth p]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3Y [auth w]501Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183431 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1Z [auth u]793Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099995 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2AA [auth v]464Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104897 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1BA [auth 1]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2CA [auth 2]895Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087365 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3DA [auth 3]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4EA [auth 4]424Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143368 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6FA [auth 5]125Homo sapiensMutation(s): 0 
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PHAROS:  Q9Y3B4
GTEx:  ENSG00000115128 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AGA [auth 6]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5HA [auth 7]86Homo sapiensMutation(s): 0 
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PHAROS:  Q9BWJ5
GTEx:  ENSG00000169976 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1IA [auth J]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinJA [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RING finger protein 113AKA [auth M]343Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125352 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologLA [auth P]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
SkipMA [auth R]540Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1NA [auth T]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologOA [auth V]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1PA [auth X]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163877 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2QA [auth Y]322Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134597 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
BUD13 homologRA [auth Z]619Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137656 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase CWC27 homologSA [auth z]472Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q6UX04 (Homo sapiens)
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PHAROS:  Q6UX04
GTEx:  ENSG00000153015 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16TA [auth x]1,041Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O60231 (Homo sapiens)
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GTEx:  ENSG00000204560 
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UniProt GroupO60231
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNA117Homo sapiens
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Entity ID: 13
MoleculeChains LengthOrganismImage
U6 snRNAM [auth F]107Homo sapiens
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Entity ID: 14
MoleculeChains LengthOrganismImage
pre-mRNAN [auth G]274unidentified adenovirus
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Entity ID: 15
MoleculeChains LengthOrganismImage
U2 snRNAO [auth H]188Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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

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VA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

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CB [auth 6],
DB [auth 6],
EB [auth 6],
FB [auth M]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth F]
BB [auth F]
WA [auth C]
XA [auth F]
YA [auth F]
AB [auth F],
BB [auth F],
WA [auth C],
XA [auth F],
YA [auth F],
ZA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

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  (Full details and data files)

  • 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