7EU0

The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 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

Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA.

Huang, K.Wu, X.X.Fang, C.L.Xu, Z.G.Zhang, H.W.Gao, J.Zhou, C.M.You, L.L.Gu, Z.X.Mu, W.H.Feng, Y.Wang, J.W.Zhang, Y.

(2021) Science 374: 1579-1586

  • DOI: https://doi.org/10.1126/science.abj9184
  • Primary Citation of Related Structures:  
    7EU0, 7EU1

  • PubMed Abstract: 

    DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RNA polymerase RDR2, produces double-stranded small interfering RNA precursors essential for establishing and maintaining DNA methylation in plants. We determined the cryo–electron microscopy structures of the Pol IV–RDR2 holoenzyme and the backtracked transcription elongation complex. These structures reveal that Pol IV and RDR2 form a complex with their active sites connected by an interpolymerase channel, through which the Pol IV–generated transcript is handed over to the RDR2 active site after being backtracked, where it is used as the template for double-stranded RNA (dsRNA) synthesis. Our results describe a ‘backtracking-triggered RNA channeling’ mechanism underlying dsRNA synthesis and also shed light on the evolutionary trajectory of eukaryotic RNA polymerases.


  • 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase IV subunit 11,510Arabidopsis thalianaMutation(s): 0 
UniProt
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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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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 3319Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q39211 (Arabidopsis thaliana)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II and IV subunit 5AD [auth E]205Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for O81098 (Arabidopsis thaliana)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 6AE [auth F]144Arabidopsis thalianaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 8BF [auth H]146Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 9AG [auth I]114Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 10H [auth J]71Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 11I [auth K]116Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II, IV and V subunit 12J [auth L]51Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-dependent RNA polymerase 2K [auth M]1,133Arabidopsis thalianaMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for O82504 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*GP*AP*GP*TP*G)-3')L [auth N]20synthetic construct
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Entity ID: 13
MoleculeChains LengthOrganismImage
RNA (39-MER)M [auth O]39synthetic construct
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (33-MER)N [auth Q]33synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*CP*GP*A)-3')O [auth R]4synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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P [auth A]
R [auth A]
S [auth B]
T [auth C]
U [auth I]
P [auth A],
R [auth A],
S [auth B],
T [auth C],
U [auth I],
V [auth I],
W [auth J],
X [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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Q [auth A],
Y [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31822001

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references