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- EMDB-52893: Flavoprotein (NUHM and NUBM)-containing state of Pichia pastoris ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52893
TitleFlavoprotein (NUHM and NUBM)-containing state of Pichia pastoris mitochondrial complex I reconstituted into proteoliposomes
Map dataFinal consensus map. Globally sharpened (postprocessed) with relion.
Sample
  • Complex: The mitochondrial complex I of Pichia pastoris reconstituted into proteoliposomes
KeywordsNADH:ubiquinone oxidoreductase nanodisc membrane protein complex / MEMBRANE PROTEIN
Biological speciesKomagataella phaffii (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsGrba DN / Hirst J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
CitationJournal: Sci Adv / Year: 2025
Title: Global conformations of complex I are distinguished by the binding of a unique interdomain bridging subunit.
Authors: Chris Seunggyu Lee / Daniel N Grba / John J Wright / Bozhidar S Ivanov / Judy Hirst /
Abstract: Complex I (CI; NADH ubiquinone oxidoreductase) is central to energy generation and metabolic homeostasis in mammalian cells but contributes to adverse outcome pathways under challenging conditions. ...Complex I (CI; NADH ubiquinone oxidoreductase) is central to energy generation and metabolic homeostasis in mammalian cells but contributes to adverse outcome pathways under challenging conditions. During ischemia, mammalian CI transitions from a turnover-ready, structurally "closed" state toward a dormant "open" state that prevents it from functioning in reverse during reperfusion to produce reactive oxygen species. Unfortunately, simpler, genetically tractable CI models do not recapitulate the same regulatory behavior, compromising mechanistic studies. Here, we report the structure of isolated CI from the yeast (-CI) and identify distinct closed and open states that resemble those of mammalian CI. Notably, a hitherto-unknown protein (NUQM) completes an interdomain bridge in only the closed state, implying that NUQM stabilizes it by restricting the conformational changes of opening. The direct correlation of NUQM binding with closed/open status in -CI provides opportunities for investigating regulatory mechanisms relevant to reversible catalysis and ischemia-reperfusion injury.
History
DepositionFeb 24, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52893.png

Downloads & links

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Map

FileDownload / File: emd_52893.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal consensus map. Globally sharpened (postprocessed) with relion.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 360 pix.
= 493.2 Å		1.37 Å/pix.
x 360 pix.
= 493.2 Å		1.37 Å/pix.
x 360 pix.
= 493.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0255
Minimum - Maximum-0.04923268 - 0.14315237
Average (Standard dev.)-0.00038922692 (±0.006090744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 493.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52893_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Mask used in final refine3D job in RElION...

Fileemd_52893_additional_1.map
AnnotationMask used in final refine3D job in RElION (initially auto-generated in cryoSPARC).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_52893_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_52893_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The mitochondrial complex I of Pichia pastoris reconstituted into...

EntireName: The mitochondrial complex I of Pichia pastoris reconstituted into proteoliposomes
Components
  • Complex: The mitochondrial complex I of Pichia pastoris reconstituted into proteoliposomes

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Supramolecule #1: The mitochondrial complex I of Pichia pastoris reconstituted into...

SupramoleculeName: The mitochondrial complex I of Pichia pastoris reconstituted into proteoliposomes
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Komagataella phaffii (fungus)

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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

Concentration0.1 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
25.0 mMNaClsodium chloride
20.0 mMMES

Details: 20 mM MES, 25 mM NaCL, pH 7 @4 degrees celsius
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 10 mA, 0.39 mBar, 15 seconds
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III
DetailsLMNG-solubilised Pichia pastoris CI reconstituted into proteoliposomes (8:1:1 ratio of DOPC:DOPE:CDL [0.5 mg total] and 20 nM final Q10).

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 854 / Average exposure time: 1.69 sec. / Average electron dose: 50.37 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 73000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 116618
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

52878


Details: Taken from higher resolution dataset in the same publication
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 20260
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 1
Software - Name: cryoSPARC (ver. 3.3.)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.0)
Details: 4 classes were run in RELION with a mask around the flavoprotein region and an increased regularisation factor of T = 50. No alignment was used in this classification.
FSC plot (resolution estimation)

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