8RMK

Cryo-EM structure of human CALHM2 in complex with synthetic nanobody SbC2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs.

Drozdzyk, K.Peter, M.Dutzler, R.

(2024) Elife 13

  • DOI: https://doi.org/10.7554/eLife.96138
  • Primary Citation of Related Structures:  
    8RMK, 8RML, 8RMM, 8RMN

  • PubMed Abstract: 

    The CALHM proteins constitute a family of large pore channels that contains six closely related paralogs in humans. Two family members, CALHM1 and 3, have been associated with the release of ATP during taste sensation. Both proteins form heteromeric channels that activate at positive potential and decreased extracellular Ca 2+ concentration. Although the structures of several family members displayed large oligomeric organizations of different size, their function has in most cases remained elusive. Our previous study has identified the paralogs CALHM2, 4 and, 6 to be highly expressed in the placenta and defined their structural properties as membrane proteins exhibiting features of large pore channels with unknown activation properties (Drożdżyk et al., 2020). Here, we investigated whether these placental paralogs would form heteromers and characterized heteromeric complexes consisting of CALHM2 and CALHM4 subunits using specific binders as fiducial markers. Both proteins assemble with different stoichiometries with the largest population containing CALHM2 as the predominant component. In these oligomers, the subunits segregate and reside in their preferred conformation found in homomeric channels. Our study has thus revealed the properties that govern the formation of CALHM heteromers in a process of potential relevance in a cellular context.


  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Zurich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium homeostasis modulator protein 2331Homo sapiensMutation(s): 0 
Gene Names: CALHM2FAM26B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HA72 (Homo sapiens)
Explore Q9HA72 
Go to UniProtKB:  Q9HA72
PHAROS:  Q9HA72
GTEx:  ENSG00000138172 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HA72
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Synthetic nanobody SbC2
B [auth L],
M,
N,
O,
P,
Q,
R,
S,
T,
U,
V
154synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLC (Subject of Investigation/LOI)
Query on PLC

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth F]
CA [auth G]
DA [auth H]
EA [auth I]
AA [auth E],
BA [auth F],
CA [auth G],
DA [auth H],
EA [auth I],
FA [auth J],
GA [auth K],
W [auth A],
X [auth B],
Y [auth C],
Z [auth D]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Structure summary