7P1K | pdb_00007p1k

Cryo EM structure of bison NHA2 in nano disc structure

PDB DOI: https://doi.org/10.2210/pdb7P1K/pdb
EM Map EMD-13163: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Bison bison
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-07-01 Released: 2022-01-26
Deposition Author(s): Matsuoka, R., Fudim, R., Jung, S., Drew, D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.64 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure, mechanism and lipid-mediated remodeling of the mammalian Na + /H + exchanger NHA2.

Matsuoka, R., Fudim, R., Jung, S., Zhang, C., Bazzone, A., Chatzikyriakidou, Y., Robinson, C.V., Nomura, N., Iwata, S., Landreh, M., Orellana, L., Beckstein, O., Drew, D.

(2022) Nat Struct Mol Biol 29: 108-120

PubMed: 35173351 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-022-00738-2
Primary Citation Related Structures:
7P1I, 7P1J, 7P1K

PubMed Abstract:
The Na ⁺/H ⁺ exchanger SLC9B2, also known as NHA2, correlates with the long-sought-after Na ⁺/Li ⁺ exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite the functional importance of NHA2, structural information and the molecular basis for its ion-exchange mechanism have been lacking. Here we report the cryo-EM structures of bison NHA2 in detergent and in nanodiscs, at 3.0 and 3.5 Å resolution, respectively. The bison NHA2 structure, together with solid-state membrane-based electrophysiology, establishes the molecular basis for electroneutral ion exchange. NHA2 consists of 14 transmembrane (TM) segments, rather than the 13 TMs previously observed in mammalian Na ⁺/H ⁺ exchangers (NHEs) and related bacterial antiporters. The additional N-terminal helix in NHA2 forms a unique homodimer interface with a large intracellular gap between the protomers, which closes in the presence of phosphoinositol lipids. We propose that the additional N-terminal helix has evolved as a lipid-mediated remodeling switch for the regulation of NHA2 activity.

Organizational Affiliation

Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

Macromolecule Content

Total Structure Weight: 122.28 kDa
Atom Count: 6,892
Modeled Residue Count: 866
Deposited Residue Count: 1,070
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mitochondrial sodium/hydrogen exchanger 9B2	A [auth B], B [auth A]	535	Bison bison	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A6P3HVI0 (Bison bison bison) Explore A0A6P3HVI0 Go to UniProtKB: A0A6P3HVI0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6P3HVI0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T7X (Subject of Investigation/LOI) Query on T7X Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	D [auth B], E [auth B], M [auth A], N [auth A]	Phosphatidylinositol C₄₇ H₈₃ O₁₃ P KRTOMQDUKGRFDJ-TWUHCGEESA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain M [auth A] Focus chain N [auth A]
Y01 (Subject of Investigation/LOI) Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain C [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain C [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain C [auth B]	C [auth B] F [auth B] G [auth B] H [auth B] I [auth A] C [auth B], F [auth B], G [auth B], H [auth B], I [auth A], J [auth A], K [auth A], L [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain C [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]