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- EMDB-62477: The postprocess Cryo-EM map of Orf2971-Ftshi complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62477
TitleThe postprocess Cryo-EM map of Orf2971-Ftshi complex
Map data
Sample
  • Complex: The complex of Orf2971-FtsHi motor
KeywordsChlamydomonas reinhardtii / protein transportation / chloroplast / lipid synthesis / Enzyme / PROTEIN TRANSPORT
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang N / Li M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Plant / Year: 2024
Title: Architecture of the ATP-driven motor for protein import into chloroplasts.
Authors: Ning Wang / Jiale Xing / Xiaodong Su / Junting Pan / Hui Chen / Lifang Shi / Long Si / Wenqiang Yang / Mei Li /
Abstract: Thousands of nuclear-encoded proteins are transported into chloroplasts through the TOC-TIC translocon that spans the chloroplast envelope membranes. A motor complex pulls the translocated proteins ...Thousands of nuclear-encoded proteins are transported into chloroplasts through the TOC-TIC translocon that spans the chloroplast envelope membranes. A motor complex pulls the translocated proteins out of the TOC-TIC complex into the chloroplast stroma by hydrolyzing ATP. The Orf2971-FtsHi complex has been suggested to serve as the ATP-hydrolyzing motor in Chlamydomonas reinhardtii, but little is known about its architecture and assembly. Here, we report the 3.2-Å resolution structure of the Chlamydomonas Orf2971-FtsHi complex. The 20-subunit complex spans the chloroplast inner envelope, with two bulky modules protruding into the intermembrane space and stromal matrix. Six subunits form a hetero-hexamer that potentially provides the pulling force through ATP hydrolysis. The remaining subunits, including potential enzymes/chaperones, likely facilitate the complex assembly and regulate its proper function. Taken together, our results provide the structural foundation for a mechanistic understanding of chloroplast protein translocation.
History
DepositionNov 20, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62477.png

Downloads & links

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Map

FileDownload / File: emd_62477.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 420 pix.
= 436.8 Å		1.04 Å/pix.
x 420 pix.
= 436.8 Å		1.04 Å/pix.
x 420 pix.
= 436.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00806
Minimum - Maximum-0.04047825 - 0.08175257
Average (Standard dev.)0.00012367948 (±0.002473376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 436.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62477_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62477_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : The complex of Orf2971-FtsHi motor

EntireName: The complex of Orf2971-FtsHi motor
Components
  • Complex: The complex of Orf2971-FtsHi motor

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Supramolecule #1: The complex of Orf2971-FtsHi motor

SupramoleculeName: The complex of Orf2971-FtsHi motor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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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

Concentration1.2 mg/mL
BufferpH: 7.4 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127613
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE

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