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- EMDB-10816: Focused refinement cryo-EM structure of the yeast mitochondrial c... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10816 | |||||||||
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Title | Focused refinement cryo-EM structure of the yeast mitochondrial complex I sub-stoichiometric sulfur transferase subunit | |||||||||
![]() | Focused refinement of sub-stoichiometric sulfur transferase | |||||||||
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![]() | NADH:Ubiquinone Oxidoreductase / sulfur transferase / sub-stoichiometric / complex I / TRANSFERASE | |||||||||
Function / homology | ![]() thiosulfate sulfurtransferase / thiosulfate sulfurtransferase activity / transsulfuration / mitochondrion Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Hirst J / Grba D | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 323.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.9 KB | Display | ![]() |
Images | ![]() | 78.6 KB | ||
Masks | ![]() | 347.6 MB | ![]() | |
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() | 276.5 MB 276.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yj5MC ![]() 6skkC ![]() 6skmC ![]() 6sknC ![]() 6slqC ![]() 6sluC ![]() 6smuC ![]() 6y9vC ![]() 6y9wC ![]() 6y9xC ![]() 6y9yC ![]() 6y9zC ![]() 6zdjC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Focused refinement of sub-stoichiometric sulfur transferase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_10816_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_10816_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : ST1 (sulfur transferase)
Entire | Name: ST1 (sulfur transferase) |
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Components |
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-Supramolecule #1: ST1 (sulfur transferase)
Supramolecule | Name: ST1 (sulfur transferase) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Rhodanese-like domain-containing protein
Macromolecule | Name: Rhodanese-like domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 34.661117 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.45 |
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Grid | Model: UltrAuFoil / Material: GOLD / Support film - Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Details: Gold grids saturated with PEG thiol reagent |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | SWISS-MODEL used to generate initial model using PDB 1RHD as a template |
Output model | ![]() PDB-6yj5: |