8WA1

The cryo-EM structure of the Nicotiana tabacum PEP-PAP-TEC2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structures of the plant plastid-encoded RNA polymerase.

Wu, X.X.Mu, W.H.Li, F.Sun, S.Y.Cui, C.J.Kim, C.Zhou, F.Zhang, Y.

(2024) Cell 187: 1127-1144.e21

  • DOI: https://doi.org/10.1016/j.cell.2024.01.026
  • Primary Citation of Related Structures:  
    8W9Z, 8WA0, 8WA1

  • PubMed Abstract: 

    Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast biogenesis from proplastids and functions as the predominant RNA polymerase in mature chloroplasts. The PEP-centered transcription apparatus comprises a bacterial-origin PEP core and more than a dozen eukaryotic-origin PEP-associated proteins (PAPs) encoded in the nucleus. Here, we determined the cryo-EM structures of Nicotiana tabacum (tobacco) PEP-PAP apoenzyme and PEP-PAP transcription elongation complexes at near-atomic resolutions. Our data show the PEP core adopts a typical fold as bacterial RNAP. Fifteen PAPs bind at the periphery of the PEP core, facilitate assembling the PEP-PAP supercomplex, protect the complex from oxidation damage, and likely couple gene transcription with RNA processing. Our results report the high-resolution architecture of the chloroplast transcription apparatus and provide the structural basis for the mechanistic and functional study of transcription regulation in chloroplasts.


  • Organizational Affiliation

    Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, 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 subunit alphaA,
T [auth a]
337Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for P06269 (Nicotiana tabacum)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,070Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for P06271 (Nicotiana tabacum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit gamma688Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A140G1Q3 (Nicotiana tabacum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PAP1(pTAC3)892Nicotiana tabacumMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat-containing protein At1g74850, chloroplastic-like860Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3ZSI0 (Nicotiana tabacum)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10-like682Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3YXM6 (Nicotiana tabacum)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
superoxide dismutase266Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4CKK0 (Nicotiana tabacum)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12-like531Nicotiana tabacumMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Fructokinase-like 1, chloroplastic486Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4CE74 (Nicotiana tabacum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14-like isoform X2507Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4D7C7 (Nicotiana tabacum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PAP8(pTAC6)331Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3X147 (Nicotiana tabacum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
superoxide dismutase303Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4CIZ9 (Nicotiana tabacum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-like protein CITRX1, chloroplasticM,
W [auth m]
178Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3YEW3 (Nicotiana tabacum)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase-like770Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4D4H1 (Nicotiana tabacum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7-like isoform X1167Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3XP85 (Nicotiana tabacum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PAP13(pTAC18)143Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S3YU01 (Nicotiana tabacum)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta''U [auth c]1,388Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for P38550 (Nicotiana tabacum)
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UniProt GroupP38550
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Fructokinase-like 2, chloroplasticV [auth i]648Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for A0A1S4BFK7 (Nicotiana tabacum)
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UniProt GroupA0A1S4BFK7
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Entity ID: 17
MoleculeChains LengthOrganismImage
DNA (24-mer)24synthetic construct
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Entity ID: 18
MoleculeChains LengthOrganismImage
DNA (24-mer)24synthetic construct
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Entity ID: 19
MoleculeChains LengthOrganismImage
RNA (27-mer)27synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaJCYJ-SHFY-2022-012

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release