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- PDB-9qg1: Natively purified Rubrerythrin 16-mer from the anaerobic extremop... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9qg1
TitleNatively purified Rubrerythrin 16-mer from the anaerobic extremophile P. furiosus
ComponentsRubrerythrin
KeywordsOXIDOREDUCTASE / Metalloprotein / oxidotic stress response / ferritin-like / rubredoxin domain.
Function / homology
Function and homology information


oxidoreductase activity / iron ion binding
Similarity search - Function
: / Rubrerythrin, rubredoxin-like domain / : / Rubrerythrin, diiron-binding domain / Rubrerythrin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesPyrococcus furiosus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSkalidis, I. / Song, W. / Howes, S. / Foerster, F.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)741.018.201 Netherlands
CitationJournal: Elife / Year: 2025
Title: Structure of an oxygen-induced tubular nanocompartment in Pyrococcus furiosus
Authors: Song, W. / Fiala, J. / Skalidis, I. / Albanese, P. / Patinios, C. / Chaillet, M.L. / Kengen, S.W. / Scheltema, R.A. / Howes, S.C. / Heck, A.J. / Forster, F.
History
DepositionMar 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rubrerythrin
B: Rubrerythrin
C: Rubrerythrin
D: Rubrerythrin
E: Rubrerythrin
F: Rubrerythrin
G: Rubrerythrin
H: Rubrerythrin
I: Rubrerythrin
J: Rubrerythrin
K: Rubrerythrin
L: Rubrerythrin
M: Rubrerythrin
N: Rubrerythrin
O: Rubrerythrin
P: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,15364
Polymers312,47316
Non-polymers2,68148
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Rubrerythrin


Mass: 19529.537 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q9UWP7
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Natively purified rubrerythrin from Pyrococcus furiosus, assembled in OSIT
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.312 MDa / Experimental value: NO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESHEPES1
2150 mMSodium ChrorideNaCl1
35 mMMagnesium ChlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 2372
Image scansWidth: 6000 / Height: 4000

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3particle selection
2SerialEMimage acquisition
4cryoSPARC3CTF correction
7UCSF ChimeraX1.5model fitting
9cryoSPARC3initial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARC3classification
12cryoSPARC3D reconstruction
13PHENIX2.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 425731 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 3PWF

3pwf


Accession code: 3PWF / Source name: PDB / Type: experimental model

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