6AHD

The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/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. 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

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084, 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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UniProt GroupQ6P2Q9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-like protein 4AF [auth O]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141759 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentG [auth C]972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 6H [auth N]941Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101161 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NHP2-like protein 1I [auth M]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100138 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp31J [auth L]499Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105618 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 1K [auth 9]800Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175467 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp3L [auth J]683Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117360 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
SmBAB [auth U],
DA [auth i],
M [auth a]
231Homo sapiensMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1BB [auth V],
EA [auth j],
N [auth b]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2FA [auth k],
O [auth c],
VA [auth P]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
SmEGA [auth l],
P [auth d],
WA [auth Q]
86Homo sapiensMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
SmFHA [auth m],
Q [auth e],
XA [auth R]
92Homo sapiensMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GIA [auth n],
R [auth f],
YA [auth S]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3CA [auth h],
S [auth g],
ZA [auth T]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinT [auth E]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
WW domain-binding protein 4U [auth X]376Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120688 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase HV [auth W]177Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000171960 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein 5W [auth A0]73Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198258 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1X [auth 0]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140259 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38AY [auth Z]312Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134748 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2Z [auth 8]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000146007 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
WD40 repeat-containing protein SMU1AA [auth Y]513Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122692 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'JA [auth o]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''KA [auth p]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1LA [auth u]793Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099995 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2MA [auth v]464Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104897 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3NA [auth w]501Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183431 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2OA [auth q]95Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204392 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3PA [auth r]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170860 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4QA [auth s]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130520 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5RA [auth t]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106355 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6SA [auth x]80Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164167 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7TA [auth y]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130332 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8UA [auth z]96Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128534 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp4CB [auth K]522Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136875 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1DB [auth 1]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3EB [auth 3]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
SF3b14a, Splicing factor 3B subunit 6FB [auth 5]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115128 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AGB [auth 6]110Homo sapiensMutation(s): 0 
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Find proteins for Q7RTV0 (Homo sapiens)
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Go to UniProtKB:  Q7RTV0
PHAROS:  Q7RTV0
GTEx:  ENSG00000100410 
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UniProt GroupQ7RTV0
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
SF3b5, Splicing factor 3B subunit 5HB [auth 7]86Homo sapiensMutation(s): 0 
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Find proteins for Q9BWJ5 (Homo sapiens)
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Go to UniProtKB:  Q9BWJ5
PHAROS:  Q9BWJ5
GTEx:  ENSG00000169976 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
SF3b145, Splicing factor 3B subunit 2IB [auth 2]895Homo sapiensMutation(s): 0 
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Find proteins for Q13435 (Homo sapiens)
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PHAROS:  Q13435
GTEx:  ENSG00000087365 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
SF3b49, Splicing factor 3B subunit 4JB [auth 4]424Homo sapiensMutation(s): 0 
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Find proteins for Q15427 (Homo sapiens)
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PHAROS:  Q15427
GTEx:  ENSG00000143368 
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UniProt GroupQ15427
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Brr2, U5 small nuclear ribonucleoprotein 200 kDa helicaseKB [auth D]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O75643 (Homo sapiens)
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Go to UniProtKB:  O75643
PHAROS:  O75643
GTEx:  ENSG00000144028 
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Entity ID: 2
MoleculeChains LengthOrganismImage
U4snRNAB [auth I]144Homo sapiens
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Entity ID: 3
MoleculeChains LengthOrganismImage
U5snRNAC [auth B]117Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
U6snRNAD [auth F]107Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
pre-mRNAE [auth G]274Homo sapiens
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Entity ID: 28
MoleculeChains LengthOrganismImage
U2snRNABA [auth H]188Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2019-11-06
    Changes: Data collection, Other
  • Version 1.3: 2020-10-14
    Changes: Structure summary
  • Version 1.4: 2021-06-30
    Changes: Database references, Source and taxonomy
  • Version 1.5: 2024-11-06
    Changes: Data collection, Database references, Structure summary