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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This is version 1.1 of the entry. See complete history. 


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: https://doi.org/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. 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 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 D3146Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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PHAROS:  P62318
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UniProt GroupP62318
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'95Homo sapiensMutation(s): 0 
Gene Names: SNRPB, COD, SNRPB1
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Find proteins for P14678 (Homo sapiens)
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UniProt GroupP14678
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FC [auth F]86Homo sapiensMutation(s): 0 
Gene Names: SNRPF, PBSCF
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein ED [auth E]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GE [auth G]84Homo sapiensMutation(s): 0 
Gene Names: SNRPG, PBSCG
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U7 snRNA-associated Sm-like protein LSm10F [auth C]123Homo sapiensMutation(s): 0 
Gene Names: LSM10
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U7 snRNA-associated Sm-like protein LSm11G [auth D]259Homo sapiensMutation(s): 0 
Gene Names: LSM11
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 3684Homo sapiensMutation(s): 0 
Gene Names: CPSF3, CPSF73
EC: 3.1.27
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 2782Homo sapiensMutation(s): 0 
Gene Names: CPSF2, CPSF100, KIAA1367
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Symplekin1,072Homo sapiensMutation(s): 0 
Gene Names: SYMPK, SPK
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Entity ID: 11
MoleculeChainsLengthOrganismImage
U7 snRNAK [auth Z]60Homo sapiens
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Entity ID: 12
MoleculeChainsLengthOrganismImage
modified H2a pre-mRNAL [auth Y]52Mus musculus
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
M [auth H],
N [auth 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 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118093
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM029832

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Author supporting evidence, Database references, Derived calculations