9VMX | pdb_00009vmx

Human PIEZO1-E756del-MDFIC

PDB DOI: https://doi.org/10.2210/pdb9VMX/pdb
EM Map EMD-65195: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-06-29 Released: 2025-07-16
Deposition Author(s): Zhang, M.F., Pei, D.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of human PIEZO1 and its slow inactivating channelopathy mutants

Pei, D.Q., Zhang, M.F.

To be published.

Macromolecule Content

Total Structure Weight: 943.52 kDa
Atom Count: 32,172
Modeled Residue Count: 3,903
Deposited Residue Count: 8,301
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Piezo-type mechanosensitive ion channel component 1	A, B, C [auth D]	2,521	Homo sapiens	Mutation(s): 0 Gene Names: PIEZO1, FAM38A, KIAA0233
UniProt & NIH Common Fund Data Resources
Find proteins for Q92508 (Homo sapiens) Explore Q92508 Go to UniProtKB: Q92508
PHAROS: Q92508 GTEx: ENSG00000103335
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92508
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MyoD family inhibitor domain-containing protein	D [auth C], E, F	246	Homo sapiens	Mutation(s): 0 Gene Names: MDFIC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P1T7 (Homo sapiens) Explore Q9P1T7 Go to UniProtKB: Q9P1T7
PHAROS: Q9P1T7 GTEx: ENSG00000135272
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9P1T7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L9Q Query on L9Q Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain M [auth D] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain M [auth D] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth B], M [auth D]	(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₁ H₈₀ N O₈ P JQKOHRZNEOQNJE-VYCVAHKRSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth D]
D12 Query on D12 Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] K [auth B] L [auth B] N [auth D] G [auth A], H [auth A], K [auth B], L [auth B], N [auth D], O [auth D], P [auth C], Q [auth C], R [auth C], S [auth E], T [auth E], U [auth E], V [auth F], W [auth F], X [auth F]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth F]