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: 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 ...

    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: PRPF8, PRPC8
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GTEx:  ENSG00000174231
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentC972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2, KIAA0031, SNRP116
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GTEx:  ENSG00000108883
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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
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GTEx:  ENSG00000144028
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinE357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40, PRP8BP, SFP38, WDR57
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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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GTEx:  ENSG00000100028
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'G [auth b], Q [auth i]231Homo sapiensMutation(s): 0 
Gene Names: SNRPB, COD, SNRPB1
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GTEx:  ENSG00000125835
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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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GTEx:  ENSG00000167088
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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: SNRPD2, SNRPD1
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Entity ID: 10
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Small nuclear ribonucleoprotein FJ [auth f], T [auth m]86Homo sapiensMutation(s): 0 
Gene Names: SNRPF, PBSCF
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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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GTEx:  ENSG00000182004
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GL [auth g], V [auth n]76Homo sapiensMutation(s): 0 
Gene Names: SNRPG, PBSCG
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GTEx:  ENSG00000143977
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'W [auth o]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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GTEx:  ENSG00000131876
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Entity ID: 17
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U2 small nuclear ribonucleoprotein B''X [auth p]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3Y [auth w]501Homo sapiensMutation(s): 0 
Gene Names: SF3A3, SAP61
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GTEx:  ENSG00000183431
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1Z [auth u]793Homo sapiensMutation(s): 0 
Gene Names: SF3A1, SAP114
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GTEx:  ENSG00000099995
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Entity ID: 20
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Splicing factor 3A subunit 2AA [auth v]464Homo sapiensMutation(s): 0 
Gene Names: SF3A2, SAP62
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GTEx:  ENSG00000104897
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1BA [auth 1]1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1, SAP155
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GTEx:  ENSG00000115524
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2CA [auth 2]895Homo sapiensMutation(s): 0 
Gene Names: SF3B2, SAP145
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GTEx:  ENSG00000087365
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3DA [auth 3]1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3, KIAA0017, SAP130
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GTEx:  ENSG00000189091
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4EA [auth 4]424Homo sapiensMutation(s): 0 
Gene Names: SF3B4, SAP49
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GTEx:  ENSG00000143368
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6FA [auth 5]125Homo sapiensMutation(s): 0 
Gene Names: SF3B6, SAP14, SF3B14, SF3B14A, CGI-110, HSPC175, HT006
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GTEx:  ENSG00000115128
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AGA [auth 6]110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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GTEx:  ENSG00000100410
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5HA [auth 7]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5, SF3B10
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GTEx:  ENSG00000169976
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1IA [auth J]848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1, CRN, CGI-201, MSTP021
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GTEx:  ENSG00000101343
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinJA [auth L]802Homo sapiensMutation(s): 0 
Gene Names: CDC5L, KIAA0432, PCDC5RP
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GTEx:  ENSG00000096401
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
RING finger protein 113AKA [auth M]343Homo sapiensMutation(s): 0 
Gene Names: RNF113A, RNF113, ZNF183
EC: 2.3.2.27
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GTEx:  ENSG00000125352
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Entity ID: 31
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Spliceosome-associated protein CWC15 homologLA [auth P]229Homo sapiensMutation(s): 0 
Gene Names: CWC15, C11orf5, AD-002, HSPC148
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GTEx:  ENSG00000150316
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
SkipMA [auth R]540Homo sapiensMutation(s): 0 
Gene Names: SNW1, SKIIP, SKIP
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GTEx:  ENSG00000100603
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1NA [auth T]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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GTEx:  ENSG00000171566
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologOA [auth V]908Homo sapiensMutation(s): 0 
Gene Names: CWC22, KIAA1604, NCM
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GTEx:  ENSG00000163510
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1PA [auth X]396Homo sapiensMutation(s): 0 
Gene Names: SNIP1
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GTEx:  ENSG00000163877
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2QA [auth Y]322Homo sapiensMutation(s): 0 
Gene Names: RBMX2, CGI-79
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GTEx:  ENSG00000134597
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
BUD13 homologRA [auth Z]619Homo sapiensMutation(s): 0 
Gene Names: BUD13
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GTEx:  ENSG00000137656
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Entity ID: 38
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Peptidyl-prolyl cis-trans isomerase CWC27 homologSA [auth z]472Homo sapiensMutation(s): 0 
Gene Names: CWC27, SDCCAG10, UNQ438/PRO871
EC: 5.2.1.8
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GTEx:  ENSG00000153015
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16TA [auth x]1041Homo sapiensMutation(s): 0 
Gene Names: DHX16, DBP2, DDX16, KIAA0577, PRP2
EC: 3.6.4.13
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GTEx:  ENSG00000204560
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNAB117Homo sapiens
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Entity ID: 13
MoleculeChainsLengthOrganismImage
U6 snRNAM [auth F]107Homo sapiens
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Entity ID: 14
MoleculeChainsLengthOrganismImage
pre-mRNAN [auth G]274unidentified adenovirus
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Entity ID: 15
MoleculeChainsLengthOrganismImage
U2 snRNAO [auth H]188Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP
Download Ideal Coordinates CCD File 
UA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N		 Ligand Interaction
GTP (Subject of Investigation/LOI)
Query on GTP
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VA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
CB [auth 6], DB [auth 6], EB [auth 6], FB [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AB [auth F], BB [auth F], WA [auth C], XA [auth F], YA [auth F], ZA [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
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  (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