[English] 日本語
Yorodumi
- EMDB-21140: Cryo-EM structure of a dimer of undecameric human CALHM2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21140
TitleCryo-EM structure of a dimer of undecameric human CALHM2
Map dataDimer of undecameric human calcium homeostasis modulator protein 2, sharpened map
Sample
  • Complex: Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecamers (22-mer; gap junction like)
    • Protein or peptide: Calcium homeostasis modulator protein 2
Keywordstaste / assembly / calcium / gap junction / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of microglial cell activation / ATP export / calcium ion import / monoatomic cation channel activity / regulation of synaptic plasticity / positive regulation of apoptotic process / plasma membrane
Similarity search - Function
Calcium homeostasis modulator family / Calcium homeostasis modulator
Similarity search - Domain/homology
Calcium homeostasis modulator protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsSyrjanen JL / Chou TH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structure and assembly of calcium homeostasis modulator proteins.
Authors: Johanna L Syrjanen / Kevin Michalski / Tsung-Han Chou / Timothy Grant / Shanlin Rao / Noriko Simorowski / Stephen J Tucker / Nikolaus Grigorieff / Hiro Furukawa /
Abstract: The biological membranes of many cell types contain large-pore channels through which a wide variety of ions and metabolites permeate. Examples include connexin, innexin and pannexin, which form gap ...The biological membranes of many cell types contain large-pore channels through which a wide variety of ions and metabolites permeate. Examples include connexin, innexin and pannexin, which form gap junctions and/or bona fide cell surface channels. The most recently identified large-pore channels are the calcium homeostasis modulators (CALHMs), through which ions and ATP permeate in a voltage-dependent manner to control neuronal excitability, taste signaling and pathologies of depression and Alzheimer's disease. Despite such critical biological roles, the structures and patterns of their oligomeric assembly remain unclear. Here, we reveal the structures of two CALHMs, chicken CALHM1 and human CALHM2, by single-particle cryo-electron microscopy (cryo-EM), which show novel assembly of the four transmembrane helices into channels of octamers and undecamers, respectively. Furthermore, molecular dynamics simulations suggest that lipids can favorably assemble into a bilayer within the larger CALHM2 pore, but not within CALHM1, demonstrating the potential correlation between pore size, lipid accommodation and channel activity.
History
DepositionDec 17, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 29, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vai
  • Surface level: 4.33
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21140.png

Downloads & links

-
Map

FileDownload / File: emd_21140.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDimer of undecameric human calcium homeostasis modulator protein 2, sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 324 pix.
= 343.44 Å		1.06 Å/pix.
x 324 pix.
= 343.44 Å		1.06 Å/pix.
x 324 pix.
= 343.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.33 / Movie #1: 4.33
Minimum - Maximum-9.888503 - 17.108803000000002
Average (Standard dev.)0.006748342 (±1.0174973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 343.43997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z343.440343.440343.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-9.88917.1090.007

-
Supplemental data

-
Additional map: unsharpened map

Fileemd_21140_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecam...

EntireName: Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecamers (22-mer; gap junction like)
Components
  • Complex: Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecamers (22-mer; gap junction like)
    • Protein or peptide: Calcium homeostasis modulator protein 2

-
Supramolecule #1: Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecam...

SupramoleculeName: Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecamers (22-mer; gap junction like)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Calcium homeostasis modulator protein 2

MacromoleculeName: Calcium homeostasis modulator protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.514957 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGGTGAALIA ENFRFLSLFF KSKDVMIFNG LVALGTVGSQ ELFSVVAFHC PCSPARNYL YGLAAIGVPA LVLFIIGIIL NNHTWNLVAE CQHRRTKNCS AAPTFLLLSS ILGRAAVAPV TWSVISLLRG E AYVCALSE ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGGTGAALIA ENFRFLSLFF KSKDVMIFNG LVALGTVGSQ ELFSVVAFHC PCSPARNYL YGLAAIGVPA LVLFIIGIIL NNHTWNLVAE CQHRRTKNCS AAPTFLLLSS ILGRAAVAPV TWSVISLLRG E AYVCALSE FVDPSSLTAR EEHFPSAHAT EILARFPCKE NPDNLSDFRE EVSRRLRYES QLFGWLLIGV VAILVFLTKC LK HYCSPLS YRQEAYWAQY RANEDQLFQR TAEVHSRVLA ANNVRRFFGF VALNKDDEEL IANFPVEGTQ PRPQWNAITG VYL YRENQG LPLYSRLHKW AQGLAGNGAA PDNVEMALLP S

UniProtKB: Calcium homeostasis modulator protein 2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4 sec before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: undecameric human CALHM2
Final reconstructionApplied symmetry - Point group: D11 (2x11 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 52737
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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