7X2U | pdb_00007x2u

Structure of a human NHE3-CHP1 complex in the autoinhibited state

PDB DOI: https://doi.org/10.2210/pdb7X2U/pdb
EM Map EMD-32971: EMDB EMDataResource

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

Deposited: 2022-02-26 Released: 2022-04-20
Deposition Author(s): Dong, Y., Li, H., Gao, Y., Zhang, X.C., Zhao, Y.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 7X2U

This is version 1.3 of the entry. See complete history.

Literature

Structure of a human NHE3-CHP1 complex in the autoinhibited state

Dong, Y., Li, H., Ilie, A., Gao, Y., Boucher, A., Zhang, X.C., Orlowski, J., Zhao, Y.

(2022) Sci Adv

Macromolecule Content

Total Structure Weight: 193.03 kDa
Atom Count: 11,861
Modeled Residue Count: 1,451
Deposited Residue Count: 1,622
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/hydrogen exchanger 3	A, B	626	Homo sapiens	Mutation(s): 0 Gene Names: SLC9A3, NHE3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P48764 (Homo sapiens) Explore P48764 Go to UniProtKB: P48764
PHAROS: P48764 GTEx: ENSG00000066230
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48764
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcineurin B homologous protein 1	C, D	185	Homo sapiens	Mutation(s): 0 Gene Names: CHP1, CHP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q99653 (Homo sapiens) Explore Q99653 Go to UniProtKB: Q99653
PHAROS: Q99653 GTEx: ENSG00000187446
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99653
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
85R (Subject of Investigation/LOI) Query on 85R Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B]	[(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate C₄₁ H₇₉ O₁₃ P IBUKXRINTKQBRQ-PLWKSVIPSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
PGT Query on PGT Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] 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] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₄₀ H₇₉ O₁₀ P KBPVYRBBONZJHF-AMAPPZPBSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB37030304

Revision History (Full details and data files)

Version 1.0: 2022-04-20
Type: Initial release
Version 1.1: 2022-04-27
Changes: Database references
Version 1.2: 2024-06-26
Changes: Data collection
Version 1.3: 2025-07-02
Changes: Data collection, Structure summary

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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.