9R8N | pdb_00009r8n

Structure of human NHE6.1 bound to PIP2 (core-TM domain)

PDB DOI: https://doi.org/10.2210/pdb9R8N/pdb
EM Map EMD-53832: EMDB EMDataResource

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

Deposited: 2025-05-16 Released: 2026-09-16
Deposition Author(s): Hansen, J.S., Pike, A.C.W., Chi, G., Wolf, G., Ingles-Prieto, A., Tranberg-Jensen, J., Ye, M., Speedman, D., Goericke, F., Sauer, D.B., Beck, H., Superti-Furga, G., Huber, K.V.M.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.33 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9R8N

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

Literature

Structure of human NHE6.1 bound to PIP2 (core-TM domain)

Hansen, J.S., Pike, A.C.W., Chi, G., Wolf, G., Ingles-Prieto, A., Tranberg-Jensen, J., Ye, M., Speedman, D., Goericke, F., Sauer, D.B., Beck, H., Superti-Furga, G., Huber, K.V.M.

To be published.

Macromolecule Content

Total Structure Weight: 178.09 kDa
Atom Count: 8,134
Modeled Residue Count: 982
Deposited Residue Count: 1,544
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Sodium/hydrogen exchanger 6	A, B	772	Homo sapiens	Mutation(s): 0 Gene Names: SLC9A6, KIAA0267, NHE6
UniProt & NIH Common Fund Data Resources
Find proteins for Q92581 (Homo sapiens) Go to UniProtKB: Q92581
PHAROS: Q92581 GTEx: ENSG00000198689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92581-2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JDN( Subject of Investigation/LOI) Query on A1JDN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	H [auth A], N [auth B]	Dipalmitoyl Phosphatidylinositol 3,5-bisphosphate C₄₁ H₈₁ O₁₉ P₃ UZMPYXSDDZXMAI-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
PCF Query on PCF Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE C₄₀ H₈₀ N O₈ P KILNVBDSWZSGLL-KXQOOQHDSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], J [auth B], K [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.33 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

Ingles-Prieto, A.

Tranberg-Jensen, J.

Superti-Furga, G.

Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	777372
Innovative Medicines Initiative	Switzerland	875510

Revision History (Full details and data files)

Version 1.0: 2026-09-16
Type: Initial release

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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.