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- EMDB-61149: RpoC2 SI domain of the spinach plastid-encoded RNA polymerase -

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Basic information

Entry
Database: EMDB / ID: EMD-61149
TitleRpoC2 SI domain of the spinach plastid-encoded RNA polymerase
Map dataAuthor said This map is a locally refined map of 8XZV/EMD-38799. Author said they masked a flexible domain of the map to get some pose information for model building. Consequently, the density of the unmasked region is fragmented and looks like noise. All the calculations were performed in cryoSPARC, which may have led to an overestimation of the resolution, especially in the case of intrinsic flexibility. Author said they can either adopt the resolution calculated by the EMDB and make corresponding revisions to the article, or we can provide the Auto-tightening mask used during the CryoSPARC refinement.
Sample
  • Complex: DNA-directed RNA polymerase subunit beta''
    • Protein or peptide: DNA-directed RNA polymerase subunit beta''
Keywordsplastid-encoded RNA polymerase / chloroplast / spinach / TRANSCRIPTION
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 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_61149.png

Downloads & links

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Map

FileDownload / File: emd_61149.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAuthor said This map is a locally refined map of 8XZV/EMD-38799. Author said they masked a flexible domain of the map to get some pose information for model building. Consequently, the density of the unmasked region is fragmented and looks like noise. All the calculations were performed in cryoSPARC, which may have led to an overestimation of the resolution, especially in the case of intrinsic flexibility. Author said they can either adopt the resolution calculated by the EMDB and make corresponding revisions to the article, or we 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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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.164
Minimum - Maximum-3.5970588 - 6.9388294
Average (Standard dev.)-0.0002098219 (±0.020308904)
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_61149_msk_1.map
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Half map: #1

Fileemd_61149_half_map_1.map
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Half map: #2

Fileemd_61149_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: DNA-directed RNA polymerase subunit beta''

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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: DNA-directed RNA polymerase subunit beta''

MacromoleculeName: DNA-directed RNA polymerase subunit beta'' / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Spinacia oleracea (spinach)
SequenceString: MAERANLVFH NKAIDGTAMK RLISRLIDHF GMAYTSHILD QLKTLGFQQA TATSISLGID DLLTIPSKGW LVQDAEQQSL ILEKHHHYG NVHAVEKLRQ SIEIWYSTSE YLRQEMNPNF RMTDPYNPVH IMSFSGARGN VSQVHQLVGM RGLMSDPQGQ M IDLPIQSN ...String:
MAERANLVFH NKAIDGTAMK RLISRLIDHF GMAYTSHILD QLKTLGFQQA TATSISLGID DLLTIPSKGW LVQDAEQQSL ILEKHHHYG NVHAVEKLRQ SIEIWYSTSE YLRQEMNPNF RMTDPYNPVH IMSFSGARGN VSQVHQLVGM RGLMSDPQGQ M IDLPIQSN LREGLSLTEY IISCYGARKG VVDTAVRTSD AGYLTRRLVE VVQHIVVRRR DCGTIRGISV SPQNSTMPER IL IQTLIGR VLADDIYMGS RCIATRNQDI GVGLVNRFIT LRTQLISIRT PFTCRSASWI CRLCYGRSPT HGGLVELGEA VGI IAGQSI GEPGTQLTLR TFHTGGVFTG GTAEHVRAPS NGKIQFNEDL VHPTRTRHGH PAFLCYIDLY VTIESDDILH NVNI PPKSF LLVQNDQYVE SEQVIAEIRA GTSTLNFKER VRKHIYSDSE GEMHWSTDVY HAPEFTYGNV HLLPKTSHLW VLSGK PYRS SVVPFSLSKD QDQMNTHSLS FEQIYISNPS VTNDQVKDKL SDSFSKKEDR ITDYSELNRI GHCNLIYPAK NLDLLA KKR RNRFIIPFQG SQERKKELMS LSGISIEIPI NGIFRKNSIF AYFDDPRYRR KSSGITKYGT IEMHSIVKKE DLIEYRG VK EFRPKYQMKV DRFFFIPEEV HILAGSSSIM VRNNSIIGVD TWITLNTRSR IGGVVRVERK KKKIELTIFS GDIHFPGE T DKISRHSGIL IPPSRKNSKD SKNLKKWIYV QRITPTKKKY FVLVRPVVPY EITDGINLAT LFPQDLLQER DNVQLRVVN YILYGNGKVT RGISDTSIQL VRTCLVLNWN QDKKGSSIEE ARGSFVEVRT NGMIQDFLKV NLVKPAISYI SKRNDPSSEK KEGSDHTNM NPFYSIYIYP KTKLQKSFNQ NQGTVRTLLG INKECQFFLI LSSSNCFRIG PFKGVKYPKE LIKKDPLIPI R NSFGPLGT ALQIANFFSF YYLITHNQIL VTNYLQLDNL KQTFQPFKFQ YYLMDENGRI YNPDPCSNII FNPFKLNWYF LH YHFCEET STKIDLGQFV CENVCITKKG THLKSGQVLI VQFDSVVIRS AKPYLATPGA TLHGHYGEII YEGDTLVTFI YEK SRSGDI TQGLPKVEQV LEVRSIDSIS INLEKRIDSW NERITRILGS PWGFLIGAEL TIAQSRISLV NKIQKVYRSQ GVQI HNRHI EIIVRQITSK VLVSEDGMSN VFLPGELIGL FRAERTGRAL EEAICYRATL LGITRASLNT QSFISEASFQ ETARV LAKA ALRGRIDWLK GLKENVVLGG MIPVGTGFKG FVHHSSQHKD IPLKTKKQNL FEGEMGDILF YHRELFESCL SKN

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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: 3.24 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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