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- EMDB-35976: Structure of in situ PSII from P. purpureum lamellae by GisSPA -

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Basic information

Entry
Database: EMDB / ID: EMD-35976
TitleStructure of in situ PSII from P. purpureum lamellae by GisSPA
Map data
Sample
  • Complex: dimeric PSII complex
Keywordsin situ / MEMBRANE PROTEIN
Biological speciesPorphyridium purpureum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhang X / Cheng J
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1301501 China
CitationJournal: Nat Commun / Year: 2023
Title: Determining protein structures in cellular lamella at pseudo-atomic resolution by GisSPA.
Authors: Jing Cheng / Tong Liu / Xin You / Fa Zhang / Sen-Fang Sui / Xiaohua Wan / Xinzheng Zhang /
Abstract: Cryo-electron tomography is a major tool used to study the structure of protein complexes in situ. However, the throughput of tilt-series image data collection is still quite low. Here, we show that ...Cryo-electron tomography is a major tool used to study the structure of protein complexes in situ. However, the throughput of tilt-series image data collection is still quite low. Here, we show that GisSPA, a GPU accelerated program, can translationally and rotationally localize the target protein complex in cellular lamellae, as prepared with a focused ion beam, using single cryo-electron microscopy images without tilt-series, and reconstruct the protein complex at near-atomic resolution. GisSPA allows high-throughput data collection without the acquisition of tilt-series images and reconstruction of the tomogram, which is essential for high-resolution reconstruction of asymmetric or low-symmetry protein complexes. We demonstrate the power of GisSPA with 3.4-Å and 3.9-Å resolutions of resolving phycobilisome and tetrameric photosystem II complex structures in cellular lamellae, respectively. In this work, we present GisSPA as a practical tool that facilitates high-resolution in situ protein structure determination.
History
DepositionApr 20, 2023-
SupersessionJun 21, 2023ID: EMD-35045
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJun 21, 2023-
Current statusJun 21, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35976.png

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Map

FileDownload / File: emd_35976.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 256 pix.
= 417.792 Å		1.63 Å/pix.
x 256 pix.
= 417.792 Å		1.63 Å/pix.
x 256 pix.
= 417.792 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
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Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-1.0339235 - 1.5303233
Average (Standard dev.)0.0031682008 (±0.08376573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 417.792 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35976_msk_1.map
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Half map: #2

Fileemd_35976_half_map_1.map
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Half map: #1

Fileemd_35976_half_map_2.map
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Sample components

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Entire : dimeric PSII complex

EntireName: dimeric PSII complex
Components
  • Complex: dimeric PSII complex

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Supramolecule #1: dimeric PSII complex

SupramoleculeName: dimeric PSII complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Porphyridium purpureum (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7
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: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 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: EMDB MAP
EMDB ID:

9976

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23410
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3.0.8), cryoSPARC (ver. 2.0))
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER

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