8XZV | pdb_00008xzv

Architecture of the spinach plastid-encoded RNA polymerase

  • Classification: TRANSCRIPTION
  • Organism(s): Spinacia oleracea
  • Mutation(s): No 

  • Deposited: 2024-01-21 Released: 2024-12-04 
  • Deposition Author(s): Wang, G.-L., Yu, L.-J., Lu, C.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Architecture of the spinach plastid-encoded RNA polymerase.

Wang, T.Wang, G.L.Fang, Y.Zhang, Y.Peng, W.Zhou, Y.Zhang, A.Yu, L.J.Lu, C.

(2024) Nat Commun 15: 9838-9838

  • DOI: https://doi.org/10.1038/s41467-024-54266-2
  • Primary Citation Related Structures: 
    8XZV

  • PubMed Abstract: 

    The plastid-encoded RNA polymerase serves as the principal transcription machinery within chloroplasts, transcribing over 80% of all primary plastid transcripts. This polymerase consists of a prokaryotic-like core enzyme known as the plastid-encoded RNA polymerase core, and is supplemented by newly evolved associated proteins known as PAPs. However, the architecture of the plastid-encoded RNA polymerase and the possible functions of PAPs remain unknown. Here, we present the cryo-electron microscopy structure of a 19-subunit plastid-encoded RNA polymerase complex derived from spinach (Spinacia oleracea). The structure shows that the plastid-encoded RNA polymerase core resembles bacterial RNA polymerase. Twelve PAPs and two additional proteins (FLN2 and pTAC18) bind at the periphery of the plastid-encoded RNA polymerase core, forming extensive interactions that may facilitate complex assembly and stability. PAPs may also protect the complex against oxidative damage and has potential functions in transcriptional regulation. This research offers a structural basis for future investigations into the functions and regulatory mechanisms governing the transcription of plastid genes.


  • Organizational Affiliation
    • State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China.

Macromolecule Content 

  • Total Structure Weight: 1,112.54 kDa 
  • Atom Count: 58,999 
  • Modeled Residue Count: 7,497 
  • Deposited Residue Count: 9,737 
  • Unique protein chains: 17

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA,
N [auth O]
335Spinacia oleraceaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P06505 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,070Spinacia oleraceaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P11703 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'677Spinacia oleraceaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P11705 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta''1,357Spinacia oleraceaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P11704 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Fructokinase-like 1, chloroplastic472Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0JBX6 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Thioredoxin-like protein CITRX, chloroplasticF,
Q [auth R]
181Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0J865 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12518Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0K7U8 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
pTAC3892Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0IP63 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2490Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0IWV5 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
pTAC6J [auth K]324Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0JNY3 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
superoxide dismutaseK [auth L]284Spinacia oleraceaMutation(s): 0 
EC: 1.15.1.1
UniProt
Find proteins for A0A9R0JVI6 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
superoxide dismutaseL [auth M]273Spinacia oleraceaMutation(s): 0 
EC: 1.15.1.1
UniProt
Find proteins for A0A9R0ISF0 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10M [auth N]678Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0JF29 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7O [auth P]170Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0I5M6 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
pTAC18P [auth Q]143Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0J252 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Fructokinase-like 2, chloroplastic isoform X2R [auth S]583Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0K533 (Spinacia oleracea)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
MurES [auth J]774Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0JYS1 (Spinacia oleracea)
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
T [auth L]FE (III) ION
Fe
VTLYFUHAOXGGBS-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
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC3401800
Ministry of Science and Technology (MoST, China)China2020YFA0907600
National Natural Science Foundation of China (NSFC)China32000444

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release