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Yorodumi- PDB-8ucj: CryoEM structure of Komagataella pastoris Cytochrome c oxidase (1... -
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-Basic information
Entry | Database: PDB / ID: 8ucj | ||||||
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Title | CryoEM structure of Komagataella pastoris Cytochrome c oxidase (11 subunits) in complex with human VMAT2 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / VMAT / SLC18 / vascular monoamine transporter / Cytochrome c oxidase-VMAT2 complex | ||||||
Function / homology | Function and homology information serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity ...serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / serotonin uptake / respiratory chain complex IV / dopamine transport / dopaminergic synapse / monoamine transmembrane transporter activity / histamine secretion by mast cell / monoamine transport / Na+/Cl- dependent neurotransmitter transporters / : / cytochrome-c oxidase / neurotransmitter transport / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / enzyme regulator activity / negative regulation of reactive oxygen species biosynthetic process / response to amphetamine / post-embryonic development / secretory granule membrane / locomotory behavior / terminal bouton / response to toxic substance / synaptic vesicle membrane / synaptic vesicle / chemical synaptic transmission / mitochondrial inner membrane / axon / intracellular membrane-bounded organelle / centrosome / dendrite / heme binding / mitochondrion / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Komagataella pastoris (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Ye, J. / Liu, B. / Li, W. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: cryoEM structure of Komagataella pastoris Cytochrome c oxidase (11 subunits) in complex with human VMAT2 Authors: Ye, J. / Liu, B. / Li, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ucj.cif.gz | 387.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ucj.ent.gz | 305.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ucj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ucj_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8ucj_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8ucj_validation.xml.gz | 65.7 KB | Display | |
Data in CIF | 8ucj_validation.cif.gz | 99.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/8ucj ftp://data.pdbj.org/pub/pdb/validation_reports/uc/8ucj | HTTPS FTP |
-Related structure data
Related structure data | 42128MC M: map data used to model this data C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55749.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC18A2 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q05940 |
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-Cytochrome c oxidase subunit ... , 11 types, 11 molecules abcdefghijk
#2: Protein | Mass: 58857.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2R0K8 |
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#3: Protein | Mass: 26886.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) |
#4: Protein | Mass: 30664.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2R0J6 |
#5: Protein | Mass: 16457.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2QT92 |
#6: Protein | Mass: 14719.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2QVW8 |
#7: Protein | Mass: 11851.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2QVA2 |
#8: Protein | Mass: 6573.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2QS38 |
#9: Protein/peptide | Mass: 5456.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2QRE4 |
#10: Protein | Mass: 6619.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: A0A1G4KPQ9 |
#11: Protein | Mass: 8890.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2QZ97 |
#12: Protein | Mass: 12518.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2QT90 |
-Non-polymers , 6 types, 10 molecules
#13: Chemical | ChemComp-CU / | ||||||||
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#14: Chemical | #15: Chemical | ChemComp-PTY / #16: Chemical | ChemComp-CUA / | #17: Chemical | ChemComp-ZN / | #18: Chemical | ChemComp-PCF / | |
-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-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: Komagataella pastoris Cytochrome c oxidase (11 subunits) in complex with human VMAT2 Type: COMPLEX / Entity ID: #1-#12 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Value: 0.246 MDa / Experimental value: YES | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Komagataella pastoris (fungus) | ||||||||||||
Buffer solution | pH: 8 | ||||||||||||
Specimen | Conc.: 5 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: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 281 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: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 63 K |
Image recording | Average exposure time: 3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4614 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141043 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
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