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- PDB-8xzv: Architecture of the spinach plastid-encoded RNA polymerase -

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Entry
Database: PDB / ID: 8xzv
TitleArchitecture of the spinach plastid-encoded RNA polymerase
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • (Fructokinase-like ...) x 2
  • (Protein PLASTID TRANSCRIPTIONALLY ACTIVE ...) x 4
  • (superoxide dismutase) x 2
  • MurE
  • Thioredoxin-like protein CITRX, chloroplastic
  • pTAC18
  • pTAC3
  • pTAC6
KeywordsTRANSCRIPTION / plastid-encoded RNA polymerase / chloroplast / spinach
Function / homology
Function and homology information


etioplast organization / plastid transcription / positive regulation of red or far-red light signaling pathway / plastid-encoded plastid RNA polymerase complex / plastid organization / thylakoid membrane organization / chloroplast nucleoid / acid-amino acid ligase activity / chloroplast organization / chloroplast thylakoid ...etioplast organization / plastid transcription / positive regulation of red or far-red light signaling pathway / plastid-encoded plastid RNA polymerase complex / plastid organization / thylakoid membrane organization / chloroplast nucleoid / acid-amino acid ligase activity / chloroplast organization / chloroplast thylakoid / disulfide oxidoreductase activity / thylakoid / protein-lysine N-methyltransferase activity / biosynthetic process / superoxide dismutase / superoxide dismutase activity / protein-disulfide reductase activity / response to light stimulus / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / cell redox homeostasis / chloroplast / ribonucleoside binding / DNA-directed RNA polymerase / kinase activity / regulation of cell shape / methylation / protein dimerization activity / cell division / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 / Protein plastid transcriptionally active 7 / PLASTID TRANSCRIPTIONALLY ACTIVE protein 6 / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / Thioredoxin-like protein CITRX, chloroplastic / (S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / : / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' ...Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 / Protein plastid transcriptionally active 7 / PLASTID TRANSCRIPTIONALLY ACTIVE protein 6 / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / Thioredoxin-like protein CITRX, chloroplastic / (S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / : / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : / Rubisco LSMT substrate-binding / MurE/MurF, N-terminal / : / SAP domain superfamily / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like / Thioredoxin / SET domain / SET domain superfamily / SET domain profile. / SET domain / S1 domain profile. / RmlC-like cupin domain superfamily / 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 / Thioredoxin domain profile. / Thioredoxin domain / S1 domain / RmlC-like jelly roll fold / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / 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 Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / Tetratricopeptide-like helical domain superfamily / Thioredoxin-like superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7 / Uncharacterized protein LOC110792506 isoform X1 / superoxide dismutase / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2 / Uncharacterized protein LOC110798943 / Thioredoxin-like protein CITRX, chloroplastic / Fructokinase-like 1, chloroplastic / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / Uncharacterized protein LOC110782000 ...: / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7 / Uncharacterized protein LOC110792506 isoform X1 / superoxide dismutase / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2 / Uncharacterized protein LOC110798943 / Thioredoxin-like protein CITRX, chloroplastic / Fructokinase-like 1, chloroplastic / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / Uncharacterized protein LOC110782000 / superoxide dismutase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase MurE homolog, chloroplastic / Fructokinase-like 2, chloroplastic isoform X2 / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta'' / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsWang, G.-L. / Yu, L.-J. / Lu, C.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
Ministry of Science and Technology (MoST, China)2020YFA0907600 China
National Natural Science Foundation of China (NSFC)32000444 China
CitationJournal: Nat Commun / Year: 2024
Title: Architecture of the spinach plastid-encoded RNA polymerase.
Authors: Tongtong Wang / Guang-Lei Wang / Ying Fang / Yi Zhang / Wenxin Peng / Yue Zhou / Aihong Zhang / Long-Jiang Yu / Congming Lu /
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 ...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.
History
DepositionJan 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase subunit beta'
D: DNA-directed RNA polymerase subunit beta''
E: Fructokinase-like 1, chloroplastic
F: Thioredoxin-like protein CITRX, chloroplastic
G: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12
H: pTAC3
I: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2
K: pTAC6
L: superoxide dismutase
M: superoxide dismutase
N: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10
O: DNA-directed RNA polymerase subunit alpha
P: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7
Q: pTAC18
R: Thioredoxin-like protein CITRX, chloroplastic
S: Fructokinase-like 2, chloroplastic isoform X2
J: MurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,112,54320
Polymers1,112,48719
Non-polymers561
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein DNA-directed RNA polymerase subunit alpha / PEP / Plastid-encoded RNA polymerase subunit alpha / RNA polymerase subunit alpha


Mass: 38571.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06505, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / PEP / Plastid-encoded RNA polymerase subunit beta / RNA polymerase subunit beta


Mass: 121050.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P11703, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / PEP / Plastid-encoded RNA polymerase subunit beta' / RNA polymerase subunit beta'


Mass: 78257.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P11705, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit beta'' / PEP / Plastid-encoded RNA polymerase subunit beta'' / RNA polymerase subunit beta''


Mass: 154507.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P11704, DNA-directed RNA polymerase

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Fructokinase-like ... , 2 types, 2 molecules ES

#5: Protein Fructokinase-like 1, chloroplastic / FLN1


Mass: 53566.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JBX6
#16: Protein Fructokinase-like 2, chloroplastic isoform X2


Mass: 65597.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0K4E6

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Protein , 7 types, 8 molecules FRHKLMQJ

#6: Protein Thioredoxin-like protein CITRX, chloroplastic


Mass: 20586.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0J865
#8: Protein pTAC3


Mass: 101669.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0IP63
#10: Protein pTAC6


Mass: 37791.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JNY3
#11: Protein superoxide dismutase


Mass: 31983.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JVI6, superoxide dismutase
#12: Protein superoxide dismutase


Mass: 31092.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0ISF0, superoxide dismutase
#15: Protein pTAC18


Mass: 17109.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0J252
#17: Protein MurE


Mass: 85420.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JYS1

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Protein PLASTID TRANSCRIPTIONALLY ACTIVE ... , 4 types, 4 molecules GINP

#7: Protein Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 / pTAC12


Mass: 59779.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0K7U8
#9: Protein Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2 / pTAC14


Mass: 56522.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0IWV5
#13: Protein Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10


Mass: 80482.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JF29
#14: Protein Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7


Mass: 19339.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0I5M6

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Non-polymers , 1 types, 1 molecules

#18: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: spinach plastid-encoded RNA polymerase / Type: COMPLEX / Entity ID: #1-#9, #17, #10-#16 / Source: NATURAL
Molecular weightValue: 0.960 MDa / Experimental value: YES
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 7.6
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS 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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180924 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00360283
ELECTRON MICROSCOPYf_angle_d0.72381662
ELECTRON MICROSCOPYf_dihedral_angle_d17.67622342
ELECTRON MICROSCOPYf_chiral_restr0.0458936
ELECTRON MICROSCOPYf_plane_restr0.00510667

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