6Y50

5'domain of human 17S U2 snRNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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, 6Y53, 6Y5Q

  • 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 requires the DEAD-box ATPase PRP5 2-7 ...

    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
Splicing factor 3A subunit 3A [auth 9]501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
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UniProt GroupQ12874
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AB [auth y]110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5C [auth x]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2D [auth 8]895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3E [auth v]1,217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1F [auth u]1,304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
HIV Tat-specific factor 1H [auth q]755Homo sapiensMutation(s): 0 
Gene Names: HTATSF1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX46I [auth p]1,031Homo sapiensMutation(s): 0 
Gene Names: DDX46KIAA0801
EC: 3.6.4.13
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Entity ID: 7
MoleculeChainsLengthOrganismImage
U2 snRNAG [auth 2]188Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth y],
K [auth y],
L [auth y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2020-07-22
    Changes: Database references