8RDJ

Plastid-encoded RNA polymerase transcription elongation complex (Integrated model)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of the plant plastid-encoded RNA polymerase.

Vergara-Cruces, A.Pramanick, I.Pearce, D.Vogirala, V.K.Byrne, M.J.Low, J.K.K.Webster, M.W.

(2024) Cell 187: 1145-1159.e21

  • DOI: https://doi.org/10.1016/j.cell.2024.01.036
  • Primary Citation of Related Structures:  
    8R5O, 8R6S, 8RAS, 8RDJ

  • PubMed Abstract: 

    Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation.


  • Organizational Affiliation

    Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
327Sinapis albaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9XQN8 (Sinapis alba)
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UniProt GroupQ9XQN8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,072Sinapis albaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P46818 (Sinapis alba)
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UniProt GroupP46818
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'680Sinapis albaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A6C0M5W0 (Sinapis alba)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta''1,373Sinapis albaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A6C0M829 (Sinapis alba)
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UniProt GroupA0A6C0M829
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PAP1911Sinapis albaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PAP2862Sinapis albaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PAP3675Sinapis albaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PAP4263Sinapis albaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PAP5529Sinapis albaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PAP6460Sinapis albaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PAP7483Sinapis albaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PAP8334Sinapis albaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PAP9297Sinapis albaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PAP10
O, P
185Sinapis albaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PAP11768Sinapis albaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PAP12162Sinapis albaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
FLN2611Sinapis albaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PTAC18140Sinapis albaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PRIN2187Sinapis albaMutation(s): 0 
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Entity ID: 20
MoleculeChains LengthOrganismImage
DNA (81-MER)V [auth X]81DNA molecule
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Entity ID: 21
MoleculeChains LengthOrganismImage
DNA (81-MER)W [auth Y]81DNA molecule
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Entity ID: 22
MoleculeChains LengthOrganismImage
RNA (40-MER)X [auth Z]40synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

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BA [auth L]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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Z [auth E]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

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AA [auth I],
CA [auth N]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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Y [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P013511/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/X01102X/1
Royal SocietyUnited KingdomRGS/R2/222157
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomNT33824

Revision History  (Full details and data files)

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