[English] 日本語
Yorodumi
- EMDB-36042: ion channel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36042
Titleion channel
Map data
Sample
  • Complex: ion channel
    • Protein or peptide: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment)
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL
Keywordsion channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / bioluminescence / generation of precursor metabolites and energy / calcium ion binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...Voltage-gated cation channel calcium and sodium / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Green fluorescent protein / Voltage dependent ion channel
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen HW
Funding support Brazil, 1 items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)31971134 Brazil
CitationJournal: To Be Published
Title: ion channel
Authors: Chen HW / Chen HW
History
DepositionApr 27, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36042.png

Downloads & links

-
Map

FileDownload / File: emd_36042.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.423
Minimum - Maximum-4.126518 - 6.7497845
Average (Standard dev.)0.0044387225 (±0.12753554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_36042_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_36042_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ion channel

EntireName: ion channel
Components
  • Complex: ion channel
    • Protein or peptide: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment)
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL

-
Supramolecule #1: ion channel

SupramoleculeName: ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: ion channel,Voltage dependent ion channel,Green fluorescent prote...

MacromoleculeName: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment)
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 90.262719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEAAAAHKAQ HRTAENSMDS LEDSTHETDA GERAQAGSTK LAWTDVVAPP PRKVVFWLPH QRKVFDFYAS QGVQYFTAFL IVSNFIFNC AEKEWDPYTD QLYQGLWRWG EFAFNTMFLI ELLINFYGIA FCFWRYNWAW NTFDLVVVAI GTLTMAEAIG G NFMPPSMA ...String:
MEAAAAHKAQ HRTAENSMDS LEDSTHETDA GERAQAGSTK LAWTDVVAPP PRKVVFWLPH QRKVFDFYAS QGVQYFTAFL IVSNFIFNC AEKEWDPYTD QLYQGLWRWG EFAFNTMFLI ELLINFYGIA FCFWRYNWAW NTFDLVVVAI GTLTMAEAIG G NFMPPSMA LIRNLRAFRI FRLFKRIKSL NKIIVSLGKA IPGVANAFVI MVIIMCIYAI LGVEFYHMTG SDGTYVTYND NV KRGLCTG DEVELGQCSL NQTVSSETAR GYTYGEEYYG TFFRALYTLF QVLTGESWSE AVARPAVFES HYDSFGPVLF YVS FIIICQ IVLINVVVAV LLDKMVEEDD SEDPEKQTVA EKLSEMLSQE HAQLREIFRT WDEDNSGTIS IKEWRKAVKS MGYR GPIDV LDQIFASMDK DHSGELDYAE IDRMLSPTAA RERRSSTHAN PKRSVKEEVV AMRAEFTDHV ARLETQIAAL VLELQ LQRK PCGAEAPAPA HSRLAHDSDG APTEPPPPAA PDHHHLEDDE DTTQRVAAAL EVLFQGPSKG EELFTGVVPI LVELDG DVN GHKFSVRGEG EGDATNGKLT LKFICTTGKL PVPWPTLVTT LTYGVQCFSR YPDHMKRHDF FKSAMPEGYV QERTISF KD DGTYKTRAEV KFEGDTLVNR IELKGIDFKE DGNILGHKLE YNFNSHNVYI TADKQKNGIK ANFKIRHNVE DGSVQLAD H YQQNTPIGDG PVLLPDNHYL STQSVLSKDP NEKRDHMVLL EFVTAAGITH GMDEWSHPQF EKGGGSGGGS GGSAWSHPQ FEK

UniProtKB: Voltage dependent ion channel, Green fluorescent protein

-
Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

-
Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 10 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81844
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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://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