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- EMDB-53127: Cryo-EM structure of natively purified Rubrerythrin isolated from... -

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Basic information

Entry
Database: EMDB / ID: EMD-53127
TitleCryo-EM structure of natively purified Rubrerythrin isolated from OSIT assemblies of the anaerobic extremophile P. furiosus
Map dataRubrerythrin tetramer isolated from OSIT, Symmetry expanded map
Sample
  • Complex: Natively purified rubrerythrin from Pyrococcus furiosus, assembled in OSIT
    • Protein or peptide: Rubrerythrin
  • Ligand: FE (III) ION
KeywordsMetalloprotein / oxidotic stress response / ferritin-like / rubredoxin domain. / OXIDOREDUCTASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSkalidis I / Song W / Howes S / Foerster F
Funding support Netherlands, 1 items
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 ML / Kengen SW / Scheltema RA / Howes SC / Heck AJ / Forster F
History
DepositionMar 13, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53127.png

Downloads & links

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Map

FileDownload / File: emd_53127.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRubrerythrin tetramer isolated from OSIT, Symmetry expanded map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.708424 - 1.1591852
Average (Standard dev.)0.0033342165 (±0.033156913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53127_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rubrerythrin tetramer isolated from OSIT, Half-map A

Fileemd_53127_half_map_1.map
AnnotationRubrerythrin tetramer isolated from OSIT, Half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rubrerythrin tetramer isolated from OSIT, Half-map B

Fileemd_53127_half_map_2.map
AnnotationRubrerythrin tetramer isolated from OSIT, Half-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 : Natively purified rubrerythrin from Pyrococcus furiosus, assemble...

EntireName: Natively purified rubrerythrin from Pyrococcus furiosus, assembled in OSIT
Components
  • Complex: Natively purified rubrerythrin from Pyrococcus furiosus, assembled in OSIT
    • Protein or peptide: Rubrerythrin
  • Ligand: FE (III) ION

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Supramolecule #1: Natively purified rubrerythrin from Pyrococcus furiosus, assemble...

SupramoleculeName: Natively purified rubrerythrin from Pyrococcus furiosus, assembled in OSIT
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 312 KDa

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Macromolecule #1: Rubrerythrin

MacromoleculeName: Rubrerythrin / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 19.529537 KDa
SequenceString:
MVVKRTMTKK FLEEAFAGES MAHMRYLIFA EKAEQEGFPN IAKLFRAIAY AEFVHAKNHF IALGKLGKTP ENLQMGIEGE TFEVEEMYP VYNKAAEFQG EKEAVRTTHY ALEAEKIHAE LYRKAKEKAE KGEDIEIKKV YICPICGYTA VDEAPEYCPV C GAPKEKFV VFE

UniProtKB: Rubrerythrin

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 48 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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: 7.4
Component:
ConcentrationFormulaName
10.0 mMHEPESHEPES
150.0 mMNaClSodium Chroride
5.0 mMMgCl2Magnesium Chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number real images: 2372 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 425731
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 250 / Avg.num./class: 1000 / Software - Name: cryoSPARC (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3pwf


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9qg1:
Natively purified Rubrerythrin 16-mer from the anaerobic extremophile P. furiosus

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