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Yorodumi- PDB-7zm7: CryoEM structure of mitochondrial complex I from Chaetomium therm... -
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-Basic information
Entry | Database: PDB / ID: 7zm7 | ||||||
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Title | CryoEM structure of mitochondrial complex I from Chaetomium thermophilum (inhibited by DDM) | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Proton transporter / Mitochondrial membrane protein / Complex | ||||||
Function / homology | Function and homology information 5'-flap endonuclease activity / replication fork reversal / single-stranded DNA helicase activity / ubiquinone-6 biosynthetic process / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding ...5'-flap endonuclease activity / replication fork reversal / single-stranded DNA helicase activity / ubiquinone-6 biosynthetic process / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / DNA helicase / response to oxidative stress / DNA repair / protein-containing complex binding / mitochondrion / ATP binding / membrane / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å | ||||||
Authors | Laube, E. / Kuehlbrandt, W. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Conformational changes in mitochondrial complex I of the thermophilic eukaryote . Authors: Eike Laube / Jakob Meier-Credo / Julian D Langer / Werner Kühlbrandt / Abstract: Mitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. ...Mitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. We report the structure of complex I from the thermophilic fungus , determined by cryoEM up to 2.4-Å resolution. We show that the complex undergoes a transition between two conformations, which we refer to as state 1 and state 2. The conformational switch is manifest in a twisting movement of the peripheral arm relative to the membrane arm, but most notably in substantial rearrangements of the Q-binding cavity and the E-channel, resulting in a continuous aqueous passage from the E-channel to subunit ND5 at the far end of the membrane arm. The conformational changes in the complex interior resemble those reported for mammalian complex I, suggesting a highly conserved, universal mechanism of coupling electron transport to proton pumping. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zm7.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7zm7.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7zm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zm7_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 7zm7_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 7zm7_validation.xml.gz | 210.8 KB | Display | |
Data in CIF | 7zm7_validation.cif.gz | 337.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/7zm7 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/7zm7 | HTTPS FTP |
-Related structure data
Related structure data | 14791MC 7zm8C 7zmbC 7zmeC 7zmgC 7zmhC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-NADH-ubiquinone oxidoreductase ... , 9 types, 9 molecules 13456CGLP
#1: Protein | Mass: 41716.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G1DJA6, NADH:ubiquinone reductase (H+-translocating) |
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#3: Protein | Mass: 16330.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G1DJ99, NADH:ubiquinone reductase (H+-translocating) |
#4: Protein | Mass: 60810.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G1DJA7, NADH:ubiquinone reductase (H+-translocating) |
#5: Protein | Mass: 75872.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids added according to map density, genome sequence and MS data. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G1DJA3, NADH:ubiquinone reductase (H+-translocating) |
#6: Protein | Mass: 24819.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G1DJ96, NADH:ubiquinone reductase (H+-translocating) |
#11: Protein | Mass: 55910.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids removed according to map density, genome sequence and MS data. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCG0 |
#15: Protein | Mass: 33377.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8U1 |
#20: Protein | Mass: 9837.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G1DJA2, NADH:ubiquinone reductase (H+-translocating) |
#23: Protein | Mass: 14836.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4Q3 |
-Protein , 16 types, 17 molecules 29DHOQRSUbcdfgijn
#2: Protein | Mass: 64129.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G1DJ98 | ||||||||||||||||||||||
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#8: Protein | Mass: 87142.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. One additional amino acid modelled according to map density and genome sequence. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SG48 | ||||||||||||||||||||||
#12: Protein | Mass: 9833.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: No entry (not annotated). Sequence modelled according to map density, genome sequence and MS data. Last five amino acids unknown and modelled as Poly-Ala Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 | ||||||||||||||||||||||
#16: Protein | Mass: 35005.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SDM6 | ||||||||||||||||||||||
#22: Protein | Mass: 15593.649 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ZMP covalently linked to Ser98. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBG9 #24: Protein | | Mass: 11636.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAY0 #25: Protein | | Mass: 15847.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Sequence renumbered (compared to entry sequence) according to map density and genome sequence. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAN0, DNA helicase #26: Protein | | Mass: 21517.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0R3 #32: Protein | | Mass: 10823.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S812 #33: Protein | | Mass: 11153.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S681 #34: Protein | | Mass: 12514.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEZ1 #36: Protein | | Mass: 10897.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acid removed according to map density, genome sequence and MS data. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1P3 #37: Protein | | Mass: 9076.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZZ2 #39: Protein | | Mass: 10857.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S569 #40: Protein | | Mass: 8760.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5C8 #41: Protein | | Mass: 20824.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids added and removed according to map density and genome sequence. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S086 |
-NADH dehydrogenase [ubiquinone] ... , 5 types, 5 molecules 8BWYh
#7: Protein | Mass: 10312.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAE9 |
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#10: Protein | Mass: 55453.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G0SA46, NADH:ubiquinone reductase (H+-translocating) |
#27: Protein | Mass: 14039.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SB83 |
#29: Protein | Mass: 23494.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S3Y7 |
#38: Protein | Mass: 15967.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Sequence renumbered (compared to entry sequence) according to map density, genome sequence and MS data. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S775 |
-NADH-ubiquinone oxidoreductase-like ... , 7 types, 7 molecules AFJKMXZ
#9: Protein | Mass: 82096.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids removed and added to sequence according to map density, genome sequence and MS data. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYA1 |
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#14: Protein | Mass: 29244.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8H4 |
#18: Protein | Mass: 21612.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S2B3 |
#19: Protein | Mass: 25549.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9I6 |
#21: Protein | Mass: 18613.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids added and removed according to map density, genome sequence and MS data. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6J1 |
#28: Protein | Mass: 21645.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0S8 |
#30: Protein | Mass: 21164.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids removed and added according to map density and genome sequence. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEF0 |
-NADH dehydrogenase (Ubiquinone)-like ... , 2 types, 2 molecules Ea
#13: Protein | Mass: 43800.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids added according to map density, genome sequence and MS data. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SB35 |
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#31: Protein | Mass: 23239.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Discrepancy with annotated entry sequence. Probably wrong intron-exon boundaries. Amino acids removed and added according to map density, genome sequence and MS data. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RXU4 |
-Oxidoreductase-like ... , 2 types, 2 molecules Io
#17: Protein | Mass: 25415.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence renumbered (compared to entry sequence). Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBG8 |
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#42: Protein | Mass: 41609.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S982 |
-Protein/peptide / Sugars , 2 types, 15 molecules e
#35: Protein/peptide | Mass: 5278.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: No entry (not annotated). Sequence modelled according to map density, genome sequence and MS data. Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
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#44: Sugar | ChemComp-LMT / |
-Non-polymers , 10 types, 1249 molecules
#43: Chemical | ChemComp-PC1 / #45: Chemical | ChemComp-CDL / #46: Chemical | ChemComp-3PE / #47: Chemical | #48: Chemical | ChemComp-SF4 / #49: Chemical | ChemComp-FMN / | #50: Chemical | ChemComp-NDP / | #51: Chemical | ChemComp-ZN / | #52: Chemical | #53: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mitochondrial NADH:ubiquinone oxidoreductase in DDM / Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 0.97 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2.11 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6503 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 126638 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37767 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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