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- EMDB-61151: MurE subunit of the spinach plastid-encoded RNA polymerase -

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Basic information

Entry
Database: EMDB / ID: EMD-61151
TitleMurE subunit of the spinach plastid-encoded RNA polymerase
Map dataDue to the high flexibility in these regions, the locally refined maps show the general outline for these two subunits, with most of the unmasked protein structure occupied by noise. All calculations were performed using CryoSPARC, which may have led to an overestimation of the resolution. Authors said they can either adopt the resolution calculated by the EMDB and make corresponding revisions to the article, or they can provide the Auto-tightening mask used during the CryoSPARC refinement.
Sample
  • Complex: DNA-directed RNA polymerase subunit beta''
    • Protein or peptide: MurE
Keywordsplastid-encoded RNA polymerase / chloroplast / spinach / TRANSCRIPTION
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsWang G-L / Yu L-J / Lu C
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 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
DepositionAug 13, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61151.png

Downloads & links

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Map

FileDownload / File: emd_61151.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDue to the high flexibility in these regions, the locally refined maps show the general outline for these two subunits, with most of the unmasked protein structure occupied by noise. All calculations were performed using CryoSPARC, which may have led to an overestimation of the resolution. Authors said they can either adopt the resolution calculated by the EMDB and make corresponding revisions to the article, or they can provide the Auto-tightening mask used during the CryoSPARC refinement.
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.62963545 - 1.7718228
Average (Standard dev.)-0.00021415412 (±0.011748626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61151_msk_1.map
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Half map: #1

Fileemd_61151_half_map_1.map
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Half map: #2

Fileemd_61151_half_map_2.map
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Sample components

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Entire : DNA-directed RNA polymerase subunit beta''

EntireName: DNA-directed RNA polymerase subunit beta''
Components
  • Complex: DNA-directed RNA polymerase subunit beta''
    • Protein or peptide: MurE

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Supramolecule #1: DNA-directed RNA polymerase subunit beta''

SupramoleculeName: DNA-directed RNA polymerase subunit beta'' / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Spinacia oleracea (spinach)

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Macromolecule #1: MurE

MacromoleculeName: MurE / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
SequenceString: MFLQPFLTLP STISSPTNSS SSSSSLHFTK PLFLRPSISL LRRKTPSAAG NYYPNPSDDD PPEAPEDSSH GVSKFGQIQR QAARARKLE EEDFEKNRSV FLDAIKDVED APENEDYSTG VSGSGDDLFG DIDKAIAQKR KEFVKKGLLK PNPPKSERVV E VADDELGQ ...String:
MFLQPFLTLP STISSPTNSS SSSSSLHFTK PLFLRPSISL LRRKTPSAAG NYYPNPSDDD PPEAPEDSSH GVSKFGQIQR QAARARKLE EEDFEKNRSV FLDAIKDVED APENEDYSTG VSGSGDDLFG DIDKAIAQKR KEFVKKGLLK PNPPKSERVV E VADDELGQ EEVVDLEEID ELQGLRVVDV SEKEEEFDDD DIDVEVSELG KNGSSSSLFD ASFDIDFDSL GNNSSNKVRI VE PSFKMTL AELLDECKVV PISVYGDLEV EITGIEHDSR LVNSGDLFVC CVDGNLCLIE ADKRGAVAVV ASKEIDIEET LGC KALVIV EDTNAALPAL AAAFFRYPTK SMSVIGITGT HGKTTAAHLI KTMYEAMGLR TGMMSSVAYY VHGDNKLDFP EANP DAVLV QKLMAKMLHN GTEAVVMEAS SNELTHTRCE EIDFDIAVFT NLSRDNSHFQ GNEEEFRVAQ AKLFSRMVDP DRHRK IVNV DDPNAPFFIA QGNPNVPVLT FALENKDADV HPLKFELSLF ETTVLVNTPQ GILEISSGLL GRHNIYNILA AVTVGI AVG APLEDIVRGI EEVDAVPGRC EVIDEEQAFG VIVDHARTPD ALSRLLDSVR ELQPRRIITV IGSCGEKERG KRPMLAK VA TDKSDVTMLT SDNQGSEDPL DILDDMLAGI GWTMQDYLKH GENDYYPPLP NGHRLFLHDI RRVAVRCAVA MGEEGDMV V VAGKGHEAYQ VDGDKKEFFD DREECREALQ YVDELHQAGI DTSEFPWRLP ESH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180924
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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