6LMT

Cryo-EM structure of the killifish CALHM1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of calcium homeostasis modulator channels in diverse oligomeric assemblies.

Demura, K.Kusakizako, T.Shihoya, W.Hiraizumi, M.Nomura, K.Shimada, H.Yamashita, K.Nishizawa, T.Taruno, A.Nureki, O.

(2020) Sci Adv 6: eaba8105-eaba8105

  • DOI: https://doi.org/10.1126/sciadv.aba8105
  • Primary Citation of Related Structures:  
    6LMT, 6LMU, 6LMV, 6LMW, 6LMX

  • PubMed Abstract: 

    Calcium homeostasis modulator (CALHM) family proteins are Ca 2+ -regulated adenosine triphosphate (ATP)-release channels involved in neural functions including neurotransmission in gustation. Here, we present the cryo-electron microscopy (EM) structures of killifish CALHM1, human CALHM2, and Caenorhabditis elegans CLHM-1 at resolutions of 2.66, 3.4, and 3.6 Å, respectively. The CALHM1 octamer structure reveals that the N-terminal helix forms the constriction site at the channel pore in the open state and modulates the ATP conductance. The CALHM2 undecamer and CLHM-1 nonamer structures show the different oligomeric stoichiometries among CALHM homologs. We further report the cryo-EM structures of the chimeric construct, revealing that the intersubunit interactions at the transmembrane domain (TMD) and the TMD-intracellular domain linker define the oligomeric stoichiometry. These findings advance our understanding of the ATP conduction and oligomerization mechanisms of CALHM channels.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium homeostasis modulator 1
A, B, C, D, E
A, B, C, D, E, F, G, H
301Oryzias latipesMutation(s): 0 
Gene Names: CALHM1
Membrane Entity: Yes 
UniProt
Find proteins for H2MCM1 (Oryzias latipes)
Explore H2MCM1 
Go to UniProtKB:  H2MCM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2MCM1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01 (Subject of Investigation/LOI)
Query on Y01

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth F]
EA [auth F]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
HA [auth G],
I [auth A],
IA [auth G],
J [auth A],
JA [auth G],
K [auth A],
KA [auth G],
L [auth A],
LA [auth H],
M [auth A],
MA [auth H],
N [auth B],
NA [auth H],
O [auth B],
P [auth B],
Q [auth B],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D],
Z [auth E]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references