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- PDB-8ucj: CryoEM structure of Komagataella pastoris Cytochrome c oxidase (1... -

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Basic information

Entry
Database: PDB / ID: 8ucj
TitleCryoEM structure of Komagataella pastoris Cytochrome c oxidase (11 subunits) in complex with human VMAT2
Components
  • (Cytochrome c oxidase subunit ...) x 11
  • Synaptic vesicular amine transporter
KeywordsMEMBRANE PROTEIN / VMAT / SLC18 / vascular monoamine transporter / Cytochrome c oxidase-VMAT2 complex
Function / homology
Function and homology information


serotonin secretion by mast cell / somato-dendritic dopamine secretion / histamine uptake / aminergic neurotransmitter loading into synaptic vesicle / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Dopamine Neurotransmitter Release Cycle ...serotonin secretion by mast cell / somato-dendritic dopamine secretion / histamine uptake / aminergic neurotransmitter loading into synaptic vesicle / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / 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 / dopamine transport / monoamine transmembrane transporter activity / histamine secretion by mast cell / monoamine transport / dopaminergic synapse / respiratory chain complex IV / mitochondrial envelope / SLC-mediated transport of neurotransmitters / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / neurotransmitter transport / electron transport coupled proton transport / negative regulation of reactive oxygen species biosynthetic process / enzyme regulator activity / secretory granule membrane / response to amphetamine / post-embryonic development / locomotory behavior / response to toxic substance / terminal bouton / synaptic vesicle / synaptic vesicle membrane / chemical synaptic transmission / oxidoreductase activity / mitochondrial inner membrane / axon / intracellular membrane-bounded organelle / heme binding / dendrite / centrosome / mitochondrion / metal ion binding / membrane / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit VIIa, fungal / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily ...Cytochrome c oxidase, subunit VIIa, fungal / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / MFS transporter superfamily
Similarity search - Domain/homology
COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / PHOSPHATIDYLETHANOLAMINE / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c oxidase subunit 7 / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial ...COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / PHOSPHATIDYLETHANOLAMINE / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c oxidase subunit 7 / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 5B / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 1 / Synaptic vesicular amine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Komagataella pastoris (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYe, J. / Liu, B. / Li, W.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart AssociationEstablished Investigator Award United States
CitationJournal: 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
DepositionSep 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptic vesicular amine transporter
a: Cytochrome c oxidase subunit 1
b: Cytochrome c oxidase subunit 2
c: Cytochrome c oxidase subunit 3
d: Cytochrome c oxidase subunit 4
e: Cytochrome c oxidase subunit 5
f: Cytochrome c oxidase subunit 6
g: Cytochrome c oxidase subunit 7
h: Cytochrome c oxidase subunit 8
i: Cytochrome c oxidase subunit 9
j: Cytochrome c oxidase subunit 12
k: Cytochrome c oxidase subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,87622
Polymers255,24412
Non-polymers5,63210
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Synaptic vesicular amine transporter


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 Cytochrome c oxidase subunit 1


Mass: 58857.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2R0K8
#3: Protein Cytochrome c oxidase subunit 2


Mass: 26886.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
#4: Protein Cytochrome c oxidase subunit 3


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 Cytochrome c oxidase subunit 4


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 Cytochrome c oxidase subunit 5


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 Cytochrome c oxidase subunit 6


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 Cytochrome c oxidase subunit 7


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 Cytochrome c oxidase subunit 8


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 Cytochrome c oxidase subunit 9


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 Cytochrome c oxidase subunit 12


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 Cytochrome c oxidase subunit 13


Mass: 12518.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: F2QT90

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Non-polymers , 6 types, 10 molecules

#13: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#16: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Komagataella pastoris Cytochrome c oxidase (11 subunits) in complex with human VMAT2
Type: COMPLEX / Entity ID: #1-#12 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.246 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Komagataella pastoris (fungus)4922
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 63 K
Image recordingAverage 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.18.2_3874:model refinement
3EPUimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141043 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00717126
ELECTRON MICROSCOPYf_angle_d1.15823298
ELECTRON MICROSCOPYf_dihedral_angle_d17.0622476
ELECTRON MICROSCOPYf_chiral_restr0.072594
ELECTRON MICROSCOPYf_plane_restr0.012856

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