7B16 | pdb_00007b16

TRPC4 in complex with inhibitor GFB-9289

PDB DOI: https://doi.org/10.2210/pdb7B16/pdb
EM Map EMD-11979: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Danio rerio
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2020-11-23 Released: 2020-12-09
Deposition Author(s): Vinayagam, D., Quentin, D., Sistel, O., Merino, F., Stabrin, M., Hofnagel, O., Ledeboer, M.W., Malojcic, G., Raunser, S.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of TRPC4 regulation by calmodulin and pharmacological agents.

Vinayagam, D., Quentin, D., Yu-Strzelczyk, J., Sitsel, O., Merino, F., Stabrin, M., Hofnagel, O., Yu, M., Ledeboer, M.W., Nagel, G., Malojcic, G., Raunser, S.

(2020) Elife 9

PubMed: 33236980 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.60603
Primary Citation Related Structures:
7B05, 7B0J, 7B0S, 7B16, 7B1G

PubMed Abstract:
Canonical transient receptor potential channels (TRPC) are involved in receptor-operated and/or store-operated Ca ²⁺ signaling. Inhibition of TRPCs by small molecules was shown to be promising in treating renal diseases. In cells, the channels are regulated by calmodulin (CaM). Molecular details of both CaM and drug binding have remained elusive so far. Here, we report structures of TRPC4 in complex with three pyridazinone-based inhibitors and CaM. The structures reveal that all the inhibitors bind to the same cavity of the voltage-sensing-like domain and allow us to describe how structural changes from the ligand-binding site can be transmitted to the central ion-conducting pore of TRPC4. CaM binds to the rib helix of TRPC4, which results in the ordering of a previously disordered region, fixing the channel in its closed conformation. This represents a novel CaM-induced regulatory mechanism of canonical TRP channels.

Organizational Affiliation

Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 424.82 kDa
Atom Count: 21,152
Modeled Residue Count: 2,572
Deposited Residue Count: 3,660
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily c member 4a	A, B, C, D	915	Danio rerio	Mutation(s): 0 Gene Names: trpc4b, trpc4a Membrane Entity: Yes
UniProt
Find proteins for U3N7D8 (Danio rerio) Explore U3N7D8 Go to UniProtKB: U3N7D8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	U3N7D8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LPP Query on LPP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	G [auth A], H [auth B], K [auth C], N [auth D]	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE C₃₅ H₆₉ O₈ P PORPENFLTBBHSG-MGBGTMOVSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
SKQ (Subject of Investigation/LOI) Query on SKQ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	E [auth A], I [auth B], L [auth C], O [auth D]	5-chloranyl-4-(4-cyclohexyl-3-oxidanylidene-piperazin-1-yl)-1~{H}-pyridazin-6-one C₁₄ H₁₉ Cl N₄ O₂ XKGWJQQBZFNYMZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	F [auth A], J [auth B], M [auth C], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]