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- PDB-8p49: Uncharacterized Q8U0N8 protein from Pyrococcus furiosus -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8p49
TitleUncharacterized Q8U0N8 protein from Pyrococcus furiosus
ComponentsQ8U0N8 protein
KeywordsUNKNOWN FUNCTION / uncharacterized / hexamer / pyrococcus / pore
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsPacesa, M. / Correia, B.E. / Levy, E.D.
Funding supportEuropean Union, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Q8U0N8 protein
B: Q8U0N8 protein
C: Q8U0N8 protein
D: Q8U0N8 protein
E: Q8U0N8 protein
F: Q8U0N8 protein


Theoretical massNumber of molelcules
Total (without water)280,4056
Polymers280,4056
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Q8U0N8 protein


Mass: 46734.129 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: PF1548 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U0N8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hexameric Q8U0N8 uncharacterized protein from Pyrococcus furiosus
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 X / Calibrated magnification: 168674 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 192 K / Temperature (min): 186 K
Image recordingAverage exposure time: 3 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1
Image scansWidth: 4096 / Height: 4096

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
1cryoSPARCv4.2.1+230403particle selection
4cryoSPARCv4.2.1+230403CTF correction
7cryoSPARCv4.2.1+230403model fitting
9cryoSPARCv4.2.1+230403model refinement
10cryoSPARCv4.2.1+230403initial Euler assignment
11cryoSPARCv4.2.1+230403final Euler assignment
12cryoSPARCv4.2.1+230403classification
13cryoSPARCv4.2.1+2304033D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3449903
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 434260 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 133.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002118245
ELECTRON MICROSCOPYf_angle_d0.421124620
ELECTRON MICROSCOPYf_chiral_restr0.0422884
ELECTRON MICROSCOPYf_plane_restr0.00343083
ELECTRON MICROSCOPYf_dihedral_angle_d11.69167057

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