7B4L | pdb_00007b4l

CryoEM structure of the human sodium proton exchanger NHA2

PDB DOI: https://doi.org/10.2210/pdb7B4L/pdb
EM Map EMD-12002: EMDB EMDataResource

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

Deposited: 2020-12-02 Released: 2022-01-12
Deposition Author(s): Woehlert, D., Kuhlbrandt, W., Yildiz, O.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 7B4L

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

Literature

CryoEM structure of the human sodium proton exchanger NHA2

Woehlert, D., Kuhlbrandt, W., Yildiz, O.

To be published.

Macromolecule Content

Total Structure Weight: 121.06 kDa
Atom Count: 7,030
Modeled Residue Count: 886
Deposited Residue Count: 1,074
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/hydrogen exchanger 9B2	A, B	537	Homo sapiens	Mutation(s): 0 Gene Names: SLC9B2, NHA2, NHEDC2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q86UD5 (Homo sapiens) Explore Q86UD5 Go to UniProtKB: Q86UD5
PHAROS: Q86UD5 GTEx: ENSG00000164038
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86UD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain M [auth A] SDF format, chain D [auth A] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain D [auth A] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain D [auth A]	D [auth A], M [auth A], N [auth B], P [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain D [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain P [auth B]
C14 Query on C14 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] Q [auth B] R [auth B] E [auth A], F [auth A], G [auth A], Q [auth B], R [auth B], S [auth B]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
UND Query on UND Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] 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 A] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [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 A] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [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 A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	UNDECANE C₁₁ H₂₄ RSJKGSCJYJTIGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain C [auth A]	C [auth A], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB807

Revision History (Full details and data files)

Version 1.0: 2022-01-12
Type: Initial release
Version 1.1: 2024-07-10
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.