8HYJ | pdb_00008hyj

A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex.

Zhang, H.W.Huang, K.Gu, Z.X.Wu, X.X.Wang, J.W.Zhang, Y.

(2023) Nat Commun 14: 3118-3118

  • DOI: https://doi.org/10.1038/s41467-023-38619-x
  • Primary Citation Related Structures: 
    8HYJ

  • PubMed Abstract: 

    De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. Here, we report a cryo-EM structure of the Pol V transcription elongation complex bound to KTF1. The structure reveals the conformation of the structural motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure also reveals structural features of Pol V that prevent it from interacting with the transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V providing a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of the DNA methylation machinery. The structure provides insight into the Pol V transcription elongation process and the role of KTF1 during Pol V transcription-coupled DNA methylation.


  • Organizational Affiliation
    • Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.

Macromolecule Content 

  • Total Structure Weight: 727.24 kDa 
  • Atom Count: 28,568 
  • Modeled Residue Count: 3,612 
  • Deposited Residue Count: 6,333 
  • Unique protein chains: 13
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase V subunit 11,976Arabidopsis thalianaMutation(s): 0 
Gene Names: NRPE1DMS5DRD3NRPD1bRMD1RPE1At2g40030T28M21.19
EC: 2.7.7.6
UniProt
Find proteins for Q5D869 (Arabidopsis thaliana)
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UniProt GroupQ5D869
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases IV and V subunit 21,172Arabidopsis thalianaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9LK40 (Arabidopsis thaliana)
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UniProt GroupQ9LK40
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases IV and V subunit 3B319Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q39212 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases IV and V subunit 4205Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q6DBA5 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase V subunit 5A222Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M1J2 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 6A144Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FJ98 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase V subunit 7178Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for A6QRA1 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II and V subunit 8A146Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for O81097 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 9A114Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q6NLH0 (Arabidopsis thaliana)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 1071Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q8LFJ6 (Arabidopsis thaliana)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 11116Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q38859 (Arabidopsis thaliana)
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UniProt GroupQ38859
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 1251Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FLM8 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein RNA-directed DNA methylation 3P [auth W]1,493Arabidopsis thalianaMutation(s): 0 
Gene Names: RDM3KTF1SPT5LAt5g04290T19N18.20
UniProt
Find proteins for F4JW79 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNA (48-MER)M [auth N]48synthetic construct
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Reference Sequence
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Entity ID: 14
MoleculeChains LengthOrganismImage
RNA (30-MER)N [auth P]30synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (48-MER)O [auth T]48synthetic construct
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16_3549:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2020YFA0907902
National Natural Science Foundation of China (NSFC)ChinaJCYJ-SHFY-2022-012

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection