[English] 日本語
Yorodumi
- PDB-8ucn: Komagataella pastoris Cytochrome c oxidase in complex with human ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ucn
TitleKomagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Histamine
Components
  • (Cytochrome c oxidase subunit ...) x 9
  • Synaptic vesicular amine transporter
KeywordsMEMBRANE PROTEIN / VMAT / SLC18 / vascular monoamine transporter / Cytochrome c oxidase-VMAT2 complex / Neurotransmitters / Histamine
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 / 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 / negative regulation of reactive oxygen species biosynthetic process / response to amphetamine / post-embryonic development / secretory granule membrane / locomotory behavior / terminal bouton / synaptic vesicle membrane / response to toxic substance / 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
Cytochrome c oxidase, subunit VIIa, fungal / : / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily ...Cytochrome c oxidase, subunit VIIa, fungal / : / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / 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 III domain / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / 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 / Major facilitator superfamily / Major Facilitator 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 domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / HISTAMINE / PHOSPHATIDYLETHANOLAMINE / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c oxidase subunit 7 / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 6, mitochondrial ...COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / HISTAMINE / PHOSPHATIDYLETHANOLAMINE / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c oxidase subunit 7 / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 5B / 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: 3.31 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: Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Histamine
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,92520
Polymers229,91610
Non-polymers5,00910
Water00
1


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

-
Components

-
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

-
Cytochrome c oxidase subunit ... , 9 types, 9 molecules abcdefghi

#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: 30561.145 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: 12970.557 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: 14519.340 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: 6490.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: A0A1G4KPQ9

-
Non-polymers , 6 types, 10 molecules

#11: Chemical ChemComp-HSM / HISTAMINE


Mass: 111.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N3 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, hormone*YM
#12: 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
#13: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#14: 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
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Histamine
Type: COMPLEX / Entity ID: #1-#10 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.225 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 / Details: Cytochrome c oxidase-VMAT2-Histamine PARTICLE
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

-
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
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

-
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: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84534 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00615563
ELECTRON MICROSCOPYf_angle_d0.88721177
ELECTRON MICROSCOPYf_dihedral_angle_d17.1122249
ELECTRON MICROSCOPYf_chiral_restr0.0572380
ELECTRON MICROSCOPYf_plane_restr0.0082586

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more