EMDB-37388: The cryo-EM structure of the Nicotiana tabacum PEP-PAP-TEC2

Basic information

Entry

Database: EMDB / ID: EMD-37388

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

Sample

• Complex: Nicotiana tabacum PEP-PAP-TEC2
  • Protein or peptide: x 18 types
  • DNA: x 2 types
  • RNA: x 1 types
• Ligand: x 3 types

• Keywords: TRANSCRIPTION / PEP / PAP

Function / homology

Function:

plastid-encoded plastid RNA polymerase complex / etioplast organization / plastid transcription / positive regulation of red or far-red light signaling pathway / plastid organization / chloroplast nucleoid / thylakoid membrane organization / chloroplast organization / acid-amino acid ligase activity / chloroplast thylakoid / disulfide oxidoreductase activity / thylakoid / protein-lysine N-methyltransferase activity / biosynthetic process / plastid / superoxide dismutase / superoxide dismutase activity / protein-disulfide reductase activity / response to light stimulus / DNA-directed RNA polymerase complex / cell redox homeostasis / chloroplast / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / 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 / DNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytoplasm

Domain/homology:

Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 / Protein plastid transcriptionally active 7 / Thioredoxin-like protein CITRX, chloroplastic / PLASTID TRANSCRIPTIONALLY ACTIVE protein 6 / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / (S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / PPR repeat / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / Smr domain / Smr domain profile. / 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 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / pfkB family of carbohydrate kinases signature 1. / PPR repeat family / Mur ligase, C-terminal / Mur ligase, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / Pentatricopeptide repeat domain / Carbohydrate/purine kinase, PfkB, conserved site / Pentatricopeptide (PPR) repeat profile. / 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 / Pentatricopeptide repeat / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like / Thioredoxin / SET domain superfamily / SET domain / 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 / S1 domain / Thioredoxin domain profile. / Thioredoxin domain / RmlC-like jelly roll fold / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / 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 / 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 / Tetratricopeptide-like helical domain superfamily / Thioredoxin-like superfamily / Nucleic acid-binding, OB-fold

Component:

DNA-directed RNA polymerase subunit gamma / Uncharacterized protein LOC107760033 / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7-like isoform X1 / Thioredoxin-like protein CITRX1, chloroplastic / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12-like / Uncharacterized protein LOC107779769 / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10-like / Pentatricopeptide repeat-containing protein At1g74850, chloroplastic-like / Fructokinase-like 2, chloroplastic / Fructokinase-like 1, chloroplastic / superoxide dismutase / superoxide dismutase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase-like / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14-like isoform X2 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta''

• Biological species: Nicotiana tabacum (common tobacco) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 2.8 Å
• Authors: Wu XX / Zhang Y

Funding support

China, 1 items

Organization	Grant number	Country
Other government	JCYJ-SHFY-2022-012	China

• Citation: Journal: Cell / Year: 2024; Title: Cryo-EM structures of the plant plastid-encoded RNA polymerase.; Authors: Xiao-Xian Wu / Wen-Hui Mu / Fan Li / Shu-Yi Sun / Chao-Jun Cui / Chanhong Kim / Fei Zhou / Yu Zhang / ; 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.

History

Deposition	Sep 6, 2023	-
Header (metadata) release	Mar 13, 2024	-
Map release	Mar 13, 2024	-
Update	Mar 13, 2024	-
Current status	Mar 13, 2024	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_37388.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.83 Å

Density

Contour Level	By AUTHOR: 0.1
Minimum - Maximum	-0.37960824 - 1.362376
Average (Standard dev.)	-0.0002392651 (±0.046108633)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 560 560 560 Spacing 560 560 560
Cell	A=B=C: 464.8 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_37388_msk_1.map

Additional map: #2

• File: emd_37388_additional_1.map

Additional map: #1

• File: emd_37388_additional_2.map

Half map: #2

• File: emd_37388_half_map_1.map