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- EMDB-50363: Perkinsus marinus Respiratory supercomplex CIV focus map -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50363
TitlePerkinsus marinus Respiratory supercomplex CIV focus map
Map data
Sample
  • Complex: respiratory supercomplex
KeywordsRespiratory supercomplex / CIV / MEMBRANE PROTEIN
Function / homology
Function and homology information


L-amino acid transmembrane transporter activity / DNA strand elongation involved in mitotic DNA replication / GINS complex / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / metallocarboxypeptidase activity / copper ion binding / proteolysis / extracellular space / zinc ion binding / membrane
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / GINS complex, subunit Psf1 / GINS, helical bundle-like domain superfamily / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) ...Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / GINS complex, subunit Psf1 / GINS, helical bundle-like domain superfamily / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin, putative / Peptidase M14 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Merozoite surface protein, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein ...Ubiquitin, putative / Peptidase M14 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Merozoite surface protein, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / GINS subunit domain-containing protein / Amino acid transporter transmembrane domain-containing protein / Cytochrome c oxidase polypeptide II / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesPerkinsus marinus (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWu F / Amunts A
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230European Union
CitationJournal: To Be Published
Title: Perkinsus marinus Respiratory supercomplex CIV focus map
Authors: Wu F / Amunts A
History
DepositionMay 23, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50363.png

Downloads & links

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Map

FileDownload / File: emd_50363.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 500 pix.
= 423.2 Å		0.85 Å/pix.
x 500 pix.
= 423.2 Å		0.85 Å/pix.
x 500 pix.
= 423.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.07477563 - 0.2067906
Average (Standard dev.)0.000089154215 (±0.0024667145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 423.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50363_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_50363_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : respiratory supercomplex

EntireName: respiratory supercomplex
Components
  • Complex: respiratory supercomplex

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Supramolecule #1: respiratory supercomplex

SupramoleculeName: respiratory supercomplex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Perkinsus marinus (eukaryote)

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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: 7.5
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: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
EMDB ID:

50354

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 296890
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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