6BQV | pdb_00006bqv

Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state

PDB DOI: https://doi.org/10.2210/pdb6BQV/pdb
EM Map EMD-7133: EMDB EMDataResource

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

Deposited: 2017-11-28 Released: 2017-12-20
Deposition Author(s): Autzen, H.E., Myasnikov, A.G., Campbell, M.G., Asarnow, D., Julius, D., Cheng, Y.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), Danish Council of Independent Research

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of the human TRPM4 ion channel in a lipid nanodisc.

Autzen, H.E., Myasnikov, A.G., Campbell, M.G., Asarnow, D., Julius, D., Cheng, Y.

(2018) Science 359: 228-232

PubMed: 29217581 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.aar4510
Primary Citation Related Structures:
6BQR, 6BQV

PubMed Abstract:
Transient receptor potential (TRP) melastatin 4 (TRPM4) is a widely expressed cation channel associated with a variety of cardiovascular disorders. TRPM4 is activated by increased intracellular calcium in a voltage-dependent manner but, unlike many other TRP channels, is permeable to monovalent cations only. Here we present two structures of full-length human TRPM4 embedded in lipid nanodiscs at ~3-angstrom resolution, as determined by single-particle cryo-electron microscopy. These structures, with and without calcium bound, reveal a general architecture for this major subfamily of TRP channels and a well-defined calcium-binding site within the intracellular side of the S1-S4 domain. The structures correspond to two distinct closed states. Calcium binding induces conformational changes that likely prime the channel for voltage-dependent opening.

Organizational Affiliation

Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.

Macromolecule Content

Total Structure Weight: 545.08 kDa
Atom Count: 29,716
Modeled Residue Count: 3,728
Deposited Residue Count: 4,872
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 M member 4	A, B, C, D	1,218	Homo sapiens	Mutation(s): 0 Gene Names: TRPM4, LTRPC4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TD43 (Homo sapiens) Explore Q8TD43 Go to UniProtKB: Q8TD43
PHAROS: Q8TD43 GTEx: ENSG00000130529
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TD43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], R [auth D], S [auth D], T [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], M [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	2.1

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM098672
National Institutes of Health/Office of the Director	United States	S10OD020054
National Institutes of Health/Office of the Director	United States	S10OD021741
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS047723
Danish Council of Independent Research	Denmark	DFF-5051-00085