6Y5Q

human 17S U2 snRNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular architecture of the human 17S U2 snRNP.

Zhang, Z.Will, C.L.Bertram, K.Dybkov, O.Hartmuth, K.Agafonov, D.E.Hofele, R.Urlaub, H.Kastner, B.Luhrmann, R.Stark, H.

(2020) Nature 583: 310-313

  • DOI: 10.1038/s41586-020-2344-3
  • Primary Citation of Related Structures:  
    6Y50, 6Y5Q, 6Y53

  • PubMed Abstract: 
  • The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing 1 . Stable addition of U2 during early spliceosome formation requ ...

    The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing 1 . Stable addition of U2 during early spliceosome formation requires the DEAD-box ATPase PRP5 2-7 . Yeast U2 small nuclear RNA (snRNA) nucleotides that form base pairs with the branch site are initially sequestered in a branchpoint-interacting stem-loop (BSL) 8 , but whether the human U2 snRNA folds in a similar manner is unknown. The U2 SF3B1 protein, a common mutational target in haematopoietic cancers 9 , contains a HEAT domain (SF3B1 HEAT ) with an open conformation in isolated SF3b 10 , but a closed conformation in spliceosomes 11 , which is required for stable interaction between U2 and the branch site. Here we report a 3D cryo-electron microscopy structure of the human 17S U2 snRNP at a core resolution of 4.1 Å and combine it with protein crosslinking data to determine the molecular architecture of this snRNP. Our structure reveals that SF3B1 HEAT interacts with PRP5 and TAT-SF1, and maintains its open conformation in U2 snRNP, and that U2 snRNA forms a BSL that is sandwiched between PRP5, TAT-SF1 and SF3B1 HEAT . Thus, substantial remodelling of the BSL and displacement of BSL-interacting proteins must occur to allow formation of the U2-branch-site helix. Our studies provide a structural explanation of why TAT-SF1 must be displaced before the stable addition of U2 to the spliceosome, and identify RNP rearrangements facilitated by PRP5 that are required for stable interaction between U2 and the branch site.


    Organizational Affiliation

    Department of Structural Dynamics, MPI for Biophysical Chemistry, Göttingen, Germany. hstark1@gwdg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5A y110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
Find proteins for Q7RTV0 (Homo sapiens)
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PHAROS:  Q7RTV0
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5 x86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
Find proteins for Q9BWJ5 (Homo sapiens)
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PHAROS:  Q9BWJ5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2 8895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
Find proteins for Q13435 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3 v1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
Find proteins for Q15393 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1 u1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
Find proteins for O75533 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX46 p1031Homo sapiensMutation(s): 0 
Gene Names: DDX46KIAA0801
EC: 3.6.4.13
Find proteins for Q7L014 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A' a255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B'' b225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6 z125Homo sapiensMutation(s): 0 
Gene Names: SF3B6SAP14SF3B14SF3B14ACGI-110HSPC175HT006
Find proteins for Q9Y3B4 (Homo sapiens)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1 6793Homo sapiensMutation(s): 0 
Gene Names: SF3A1SAP114
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2 7464Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
Find proteins for Q15428 (Homo sapiens)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3 9501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4 o424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
Find proteins for Q15427 (Homo sapiens)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B' m240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G k76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1 n119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2 h118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 l126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E j92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F i86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
HIV Tat-specific factor 1 q755Homo sapiensMutation(s): 0 
Gene Names: HTATSF1
Find proteins for O43719 (Homo sapiens)
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Entity ID: 22
MoleculeChainsLengthOrganismImage
U2snRNA2188Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History 

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references