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- EMDB-39948: Cryo-EM Map of Pisum sativum TOC-TIC-Ycf2-FtsHi Ultracomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-39948
TitleCryo-EM Map of Pisum sativum TOC-TIC-Ycf2-FtsHi Ultracomplex
Map data
Sample
  • Complex: Pisum sativum TOC-TIC-Ycf2-FtsHi Ultracomplex
KeywordsComplex / Translocase / Channel / Membrane protein.
Biological speciesPisum sativum (garden pea)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsWu J / Yan Z / Li Y / Jin Z / Xu Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2024
Title: Structural insights into the chloroplast protein import in land plants.
Authors: Ke Liang / Zeyu Jin / Xiechao Zhan / Yuxin Li / Qikui Xu / Yanqiu Xie / Yi Yang / Shaojie Wang / Jianping Wu / Zhen Yan /
Abstract: Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi ...Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi complex has been identified as the chloroplast import motor. However, its assembly and cooperation with the TIC complex during preprotein translocation remain unclear. Here, we present the structures of the Ycf2-FtsHi and TIC complexes from Arabidopsis and an ultracomplex formed between them from Pisum. The Ycf2-FtsHi structure reveals a heterohexameric AAA+ ATPase motor module with characteristic features. Four previously uncharacterized components of Ycf2-FtsHi were identified, which aid in complex assembly and anchoring of the motor module at a tilted angle relative to the membrane. When considering the structures of the TIC complex and the TIC-Ycf2-FtsHi ultracomplex together, it becomes evident that the tilted motor module of Ycf2-FtsHi enables its close contact with the TIC complex, thereby facilitating efficient preprotein translocation. Our study provides valuable structural insights into the chloroplast protein import process in land plants.
History
DepositionApr 30, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39948.png

Downloads & links

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Map

FileDownload / File: emd_39948.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 480 pix.
= 521.76 Å		1.09 Å/pix.
x 480 pix.
= 521.76 Å		1.09 Å/pix.
x 480 pix.
= 521.76 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.281
Minimum - Maximum-0.6929845 - 1.5831506
Average (Standard dev.)0.0022125035 (±0.04475319)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 521.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39948_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39948_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Pisum sativum TOC-TIC-Ycf2-FtsHi Ultracomplex

EntireName: Pisum sativum TOC-TIC-Ycf2-FtsHi Ultracomplex
Components
  • Complex: Pisum sativum TOC-TIC-Ycf2-FtsHi Ultracomplex

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Supramolecule #1: Pisum sativum TOC-TIC-Ycf2-FtsHi Ultracomplex

SupramoleculeName: Pisum sativum TOC-TIC-Ycf2-FtsHi Ultracomplex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pisum sativum (garden pea)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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: 1.5 µm
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: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31661
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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