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- EMDB-17402: Uncharacterized Q8U0N8 protein from Pyrococcus furiosus -

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Basic information

Entry
Database: EMDB / ID: EMD-17402
TitleUncharacterized Q8U0N8 protein from Pyrococcus furiosus
Map dataQ8U0N8
Sample
  • Complex: Hexameric Q8U0N8 uncharacterized protein from Pyrococcus furiosus
    • Protein or peptide: Q8U0N8 protein
Keywordsuncharacterized / hexamer / pyrococcus / pore / UNKNOWN FUNCTION
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsPacesa M / Correia BE / Levy ED
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Cell / Year: 2024
Title: An atlas of protein homo-oligomerization across domains of life.
Authors: Hugo Schweke / Martin Pacesa / Tal Levin / Casper A Goverde / Prasun Kumar / Yoan Duhoo / Lars J Dornfeld / Benjamin Dubreuil / Sandrine Georgeon / Sergey Ovchinnikov / Derek N Woolfson / ...Authors: Hugo Schweke / Martin Pacesa / Tal Levin / Casper A Goverde / Prasun Kumar / Yoan Duhoo / Lars J Dornfeld / Benjamin Dubreuil / Sandrine Georgeon / Sergey Ovchinnikov / Derek N Woolfson / Bruno E Correia / Sucharita Dey / Emmanuel D Levy /
Abstract: Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their ...Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes.
History
DepositionMay 19, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17402.png

Downloads & links

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Map

FileDownload / File: emd_17402.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationQ8U0N8
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 380 pix.
= 315.4 Å		0.83 Å/pix.
x 380 pix.
= 315.4 Å		0.83 Å/pix.
x 380 pix.
= 315.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.2874146 - 0.5562425
Average (Standard dev.)-0.00037325802 (±0.013292744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 315.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17402_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_17402_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_17402_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexameric Q8U0N8 uncharacterized protein from Pyrococcus furiosus

EntireName: Hexameric Q8U0N8 uncharacterized protein from Pyrococcus furiosus
Components
  • Complex: Hexameric Q8U0N8 uncharacterized protein from Pyrococcus furiosus
    • Protein or peptide: Q8U0N8 protein

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Supramolecule #1: Hexameric Q8U0N8 uncharacterized protein from Pyrococcus furiosus

SupramoleculeName: Hexameric Q8U0N8 uncharacterized protein from Pyrococcus furiosus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)

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Macromolecule #1: Q8U0N8 protein

MacromoleculeName: Q8U0N8 protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 46.734129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSESINNITK PKERRDFVVM AGMRKDGTID FIKVYALNEK LAIEVLEAFL KENNIHPSDF IVIQRGYEDV KDKKAITTRS EEELSAMLG RLGLRLVSNG VLYTDGIDKL YQITAISREL FESLQKEKRE IFEDVQEKIT FNFSKVDLPE KYVKKLRLLE L MEDTIIFN ...String:
MSESINNITK PKERRDFVVM AGMRKDGTID FIKVYALNEK LAIEVLEAFL KENNIHPSDF IVIQRGYEDV KDKKAITTRS EEELSAMLG RLGLRLVSNG VLYTDGIDKL YQITAISREL FESLQKEKRE IFEDVQEKIT FNFSKVDLPE KYVKKLRLLE L MEDTIIFN MAELEIPNLL KAIVEGTVLI PRFLEKEDLI IRIFDEELHE YRGSYFDKVL IKPPIIHWDF YLDSLEDFSF KK VEESIYI APLFLRATGG FLILTEPPED LVKTLLKLKK RGEVRTILEG KRITIPINFT LIVDTRHPER YAGLKFPIRI NLP PLDDET FLKVLETNLG ITPPTEIVRI FPPDYKTFLG VELIKNLFEK LKLTEKGKDE VSLLKEAATI ITGGTPGGSS GGSG HHHHH H

UniProtKB: Uncharacterized protein

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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

Concentration4 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 168674 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000
Sample stageCooling holder cryogen: NITROGEN
TemperatureMin: 186.0 K / Max: 192.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3449903
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1+230403)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.2.1+230403)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1+230403)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.1+230403) / Number images used: 434260
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8p49:
Uncharacterized Q8U0N8 protein from Pyrococcus furiosus

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