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- PDB-8ras: Plastid-encoded RNA polymerase transcription elongation complex -

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Basic information

Entry
Database: PDB / ID: 8ras
TitlePlastid-encoded RNA polymerase transcription elongation complex
Components
  • (DNA (81-MER)) x 2
  • (DNA-directed RNA polymerase subunit ...) x 4
  • FLN2
  • PAP1
  • PAP10
  • PAP11
  • PAP12
  • PAP2
  • PAP3
  • PAP4
  • PAP5
  • PAP6
  • PAP7
  • PAP8
  • PAP9
  • PTAC18
  • RNA (40-MER)
KeywordsGENE REGULATION / Transcription / chloroplast / RNA polymerase / photosynthesis
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / chloroplast / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding
Similarity search - Function
: / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily ...: / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta''
Similarity search - Component
Biological speciesSinapis alba (white mustard)
DNA molecule (others)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsWebster, M.W. / Pramanick, I. / Vergara-Cruces, A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P013511/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01102X/1 United Kingdom
Royal SocietyRGS/R2/222157 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)NT33824 United Kingdom
CitationJournal: Cell / Year: 2024
Title: Structure of the plant plastid-encoded RNA polymerase.
Authors: Ángel Vergara-Cruces / Ishika Pramanick / David Pearce / Vinod K Vogirala / Matthew J Byrne / Jason K K Low / Michael W Webster /
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 ...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.
History
DepositionDec 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit beta''
F: PAP1
G: PAP2
H: PAP3
I: PAP4
J: PAP5
K: PAP6
L: PAP7
M: PAP8
N: PAP9
O: PAP10
P: PAP10
Q: PAP11
R: PAP12
S: FLN2
T: PTAC18
X: DNA (81-MER)
Y: DNA (81-MER)
Z: RNA (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,277,07528
Polymers1,276,48923
Non-polymers5865
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

#1: Protein DNA-directed RNA polymerase subunit alpha


Mass: 37945.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) / References: UniProt: A0A6C0M610
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 121209.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) / References: UniProt: A0A6C0M5W1
#3: Protein DNA-directed RNA polymerase subunit beta' / PEP / Plastid-encoded RNA polymerase subunit beta' / RNA polymerase subunit beta'


Mass: 78761.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
References: UniProt: A0A6C0M5W0, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit beta''


Mass: 156388.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) / References: UniProt: A0A6C0M829

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Protein , 14 types, 15 molecules FGHIJKLMNOPQRST

#5: Protein PAP1


Mass: 103467.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#6: Protein PAP2


Mass: 96112.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#7: Protein PAP3


Mass: 79815.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#8: Protein PAP4


Mass: 30273.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#9: Protein PAP5


Mass: 60884.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#10: Protein PAP6


Mass: 52435.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#11: Protein PAP7


Mass: 55675.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#12: Protein PAP8


Mass: 38039.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#13: Protein PAP9


Mass: 34008.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#14: Protein PAP10


Mass: 20954.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#15: Protein PAP11


Mass: 85121.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#16: Protein PAP12


Mass: 18835.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#17: Protein FLN2


Mass: 68527.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#18: Protein PTAC18


Mass: 16429.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)

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DNA chain , 2 types, 2 molecules XY

#19: DNA chain DNA (81-MER)


Mass: 25062.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#20: DNA chain DNA (81-MER)


Mass: 24821.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

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RNA chain , 1 types, 1 molecules Z

#21: RNA chain RNA (40-MER)


Mass: 12819.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 259 molecules

#22: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#26: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Plastid-encoded RNA polymerase transcription elongation complex
Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL
Source (natural)Organism: Sinapis alba (white mustard)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40.48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 417374 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00358496
ELECTRON MICROSCOPYf_angle_d0.49979419
ELECTRON MICROSCOPYf_dihedral_angle_d10.7048332
ELECTRON MICROSCOPYf_chiral_restr0.0418612
ELECTRON MICROSCOPYf_plane_restr0.0049969

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