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- EMDB-10816: Focused refinement cryo-EM structure of the yeast mitochondrial c... -

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Basic information

Entry
Database: EMDB / ID: EMD-10816
TitleFocused refinement cryo-EM structure of the yeast mitochondrial complex I sub-stoichiometric sulfur transferase subunit
Map dataFocused refinement of sub-stoichiometric sulfur transferase
Sample
  • Complex: ST1 (sulfur transferase)
    • Protein or peptide: Rhodanese-like domain-containing protein
KeywordsNADH:Ubiquinone Oxidoreductase / sulfur transferase / sub-stoichiometric / complex I / TRANSFERASE
Function / homology
Function and homology information


3-mercaptopyruvate sulfurtransferase activity / tRNA wobble position uridine thiolation / thiosulfate-cyanide sulfurtransferase activity / mitochondrion
Similarity search - Function
Sulfurtransferase TST/MPST-like / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain
Similarity search - Domain/homology
Rhodanese-like domain-containing protein / YALI0F23551p
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHirst J / Grba D
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105663141 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation.
Authors: Daniel N Grba / Judy Hirst /
Abstract: Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. ...Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. Recent cryo-EM analyses of mammalian and yeast complex I have revolutionized structural and mechanistic knowledge and defined structures in different functional states. Here, we describe a 2.7-Å-resolution structure of the 42-subunit complex I from the yeast Yarrowia lipolytica containing 275 structured water molecules. We identify a proton-relay pathway for ubiquinone reduction and water molecules that connect mechanistically crucial elements and constitute proton-translocation pathways through the membrane. By comparison with known structures, we deconvolute structural changes governing the mammalian 'deactive transition' (relevant to ischemia-reperfusion injury) and their effects on the ubiquinone-binding site and a connected cavity in ND1. Our structure thus provides important insights into catalysis by this enigmatic respiratory machine.
History
DepositionApr 2, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0475
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0475
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yj5
  • Surface level: 0.0475
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yj5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10816.png

Downloads & links

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Map

FileDownload / File: emd_10816.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement of sub-stoichiometric sulfur transferase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 450 pix.
= 474.75 Å		1.06 Å/pix.
x 450 pix.
= 474.75 Å		1.06 Å/pix.
x 450 pix.
= 474.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0475 / Movie #1: 0.0475
Minimum - Maximum-0.10889156 - 0.17846541
Average (Standard dev.)-0.000044474702 (±0.0044187894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 474.74997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z474.750474.750474.750
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.1090.178-0.000

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Supplemental data

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Mask #1

Fileemd_10816_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_10816_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_10816_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 : ST1 (sulfur transferase)

EntireName: ST1 (sulfur transferase)
Components
  • Complex: ST1 (sulfur transferase)
    • Protein or peptide: Rhodanese-like domain-containing protein

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Supramolecule #1: ST1 (sulfur transferase)

SupramoleculeName: ST1 (sulfur transferase) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Yarrowia lipolytica (yeast)

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Macromolecule #1: Rhodanese-like domain-containing protein

MacromoleculeName: Rhodanese-like domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 34.661117 KDa
Recombinant expressionOrganism: Yarrowia lipolytica (yeast)
SequenceString: MSKLISPAEL AKRLSSKETK IFDATWYLPT PANVGKNAYD NYMKKRIPGA LYFDIDAVNT PSKFPHMLPS PQTFENELTK LGVSSDSPI VVYDTQGVFS GPRLVWTFKV FGHDNVQFLN GFEAYTQLPG IPSRPDAYTW GIWDTQVPGK IDPADPPYKV T KARPELVK ...String:
MSKLISPAEL AKRLSSKETK IFDATWYLPT PANVGKNAYD NYMKKRIPGA LYFDIDAVNT PSKFPHMLPS PQTFENELTK LGVSSDSPI VVYDTQGVFS GPRLVWTFKV FGHDNVQFLN GFEAYTQLPG IPSRPDAYTW GIWDTQVPGK IDPADPPYKV T KARPELVK SFEDVLAIVE KHNGDGAKIR NEVTFIDARP NGRFTGKDAE PRAELSSGHV PGAYSIAFPE VVENGKFKSP EE LKALFAS KGIDGSKPII SMCGSGVTAC VIDLALEIAG IGSRDTNAVY DGSWTEWAQR APTKYIVKEE NLNEANRA

UniProtKB: Rhodanese-like domain-containing 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

BufferpH: 7.45
GridModel: UltrAuFoil / Material: GOLD / Support film - Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Details: Gold grids saturated with PEG thiol reagent
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2540 / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: -2.7 µm / Calibrated defocus min: -1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 106302 / Details: After manual curation of Relion auto-pick
Startup modelType of model: EMDB MAP
Details: Low-pass filtered (60 angstrom) of in-house map from previous work.
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 25456
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Details: Initial 2D classification to remove junk particles, followed by the same in 3D space.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: Using Relion 3D Refinement with solvent flattening
Final 3D classificationNumber classes: 2 / Avg.num./class: 25000 / Software - Name: RELION (ver. 3.1)
Details: around 50 percentage of final good particles contained this sub-stoichiometric subunit.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1rhd


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsSWISS-MODEL used to generate initial model using PDB 1RHD as a template
Output model

PDB-6yj5:
Focused refinement cryo-EM structure of the yeast mitochondrial complex I sub-stoichiometric sulfur transferase subunit

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