6V4X

Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structure of an active human histone pre-mRNA 3'-end processing machinery.

Sun, Y.Zhang, Y.Aik, W.S.Yang, X.C.Marzluff, W.F.Walz, T.Dominski, Z.Tong, L.

(2020) Science 367: 700-703

  • DOI: 10.1126/science.aaz7758
  • Primary Citation of Related Structures:  
    6V4X

  • PubMed Abstract: 
  • The 3'-end processing machinery for metazoan replication-dependent histone precursor messenger RNAs (pre-mRNAs) contains the U7 small nuclear ribonucleoprotein and shares the key cleavage module with the canonical cleavage and polyadenylation machinery. ...

    The 3'-end processing machinery for metazoan replication-dependent histone precursor messenger RNAs (pre-mRNAs) contains the U7 small nuclear ribonucleoprotein and shares the key cleavage module with the canonical cleavage and polyadenylation machinery. We reconstituted an active human histone pre-mRNA processing machinery using 13 recombinant proteins and two RNAs and determined its structure by cryo-electron microscopy. The overall structure is highly asymmetrical and resembles an amphora with one long handle. We captured the pre-mRNA in the active site of the endonuclease, the 73-kilodalton subunit of the cleavage and polyadenylation specificity factor, poised for cleavage. The endonuclease and the entire cleavage module undergo extensive rearrangements for activation, triggered through the recognition of the duplex between the authentic pre-mRNA and U7 small nuclear RNA (snRNA). Our study also has notable implications for understanding canonical and snRNA 3'-end processing.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA. ltong@columbia.edu zbigniew_dominski@med.unc.edu twalz@rockefeller.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 A146Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
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PHAROS:  P62318
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B' B95Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
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PHAROS:  P14678
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F F86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
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PHAROS:  P62306
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E E92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
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PHAROS:  P62304
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G G84Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U7 snRNA-associated Sm-like protein LSm10 C123Homo sapiensMutation(s): 0 
Gene Names: LSM10
Find proteins for Q969L4 (Homo sapiens)
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PHAROS:  Q969L4
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U7 snRNA-associated Sm-like protein LSm11 D259Homo sapiensMutation(s): 0 
Gene Names: LSM11
Find proteins for P83369 (Homo sapiens)
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PHAROS:  P83369
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 3 H684Homo sapiensMutation(s): 0 
Gene Names: CPSF3CPSF73
EC: 3.1.27
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PHAROS:  Q9UKF6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 2 I782Homo sapiensMutation(s): 0 
Gene Names: CPSF2CPSF100KIAA1367
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PHAROS:  Q9P2I0
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Symplekin J1072Homo sapiensMutation(s): 0 
Gene Names: SYMPKSPK
Find proteins for Q92797 (Homo sapiens)
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  • Reference Sequence
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Entity ID: 11
MoleculeChainsLengthOrganismImage
U7 snRNAZ60Homo sapiens
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Entity ID: 12
MoleculeChainsLengthOrganismImage
modified H2a pre-mRNAY52Mus musculus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35GM118093
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM029832

Revision History 

  • Version 1.0: 2020-02-19
    Type: Initial release