9Y9D | pdb_00009y9d

Cryo-EM structure of wild-type human CNNM4 tetramer with Magnesium and MgATP in outward-facing state

PDB DOI: https://doi.org/10.2210/pdb9Y9D/pdb
EM Map EMD-72694: EMDB EMDataResource

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

Deposited: 2025-09-14 Released: 2026-07-29
Deposition Author(s): Bai, Z., Zhou, E., Lu, W., Du, J.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.48 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

Dynamic dimer-of-dimers architecture defines Mg2+ transport in human CNNM4

Bai, Z., Zhou, E., Lu, W., Du, J.

To be published.

Macromolecule Content

Total Structure Weight: 383.4 kDa
Atom Count: 20,658
Modeled Residue Count: 2,552
Deposited Residue Count: 3,376
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal transporter CNNM4	A, B, C, D	844	Homo sapiens	Mutation(s): 0 Gene Names: CNNM4, ACDP4, KIAA1592
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P4Q7 (Homo sapiens) Explore Q6P4Q7 Go to UniProtKB: Q6P4Q7
GTEx: ENSG00000158158
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6P4Q7
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q6P4Q7-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H, I E, F, G, H, I, J, K, L	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain JA [auth D] SDF format, chain M [auth A] SDF format, chain U [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B]	BA [auth C], JA [auth D], M [auth A], U [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain BA [auth C] Focus chain JA [auth D] Focus chain M [auth A] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain JA [auth D] Focus chain M [auth A] Focus chain U [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain IA [auth C] SDF format, chain PA [auth D] SDF format, chain T [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain T [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain PA [auth D] mmCIF format, chain T [auth A]	AA [auth B], IA [auth C], PA [auth D], T [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain IA [auth C] Focus chain PA [auth D] Focus chain T [auth A] Interactions & Density Focus chain AA [auth B] Focus chain IA [auth C] Focus chain PA [auth D] Focus chain T [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] KA [auth D] CA [auth C], DA [auth C], EA [auth C], FA [auth C], KA [auth D], LA [auth D], MA [auth D], N [auth A], NA [auth D], O [auth A], P [auth A], Q [auth A], V [auth B], W [auth B], X [auth B], Y [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain OA [auth D] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain Z [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Z [auth B]	GA [auth C] HA [auth C] OA [auth D] R [auth A] S [auth A] GA [auth C], HA [auth C], OA [auth D], R [auth A], S [auth A], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain OA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain Z [auth B] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain OA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	RELION	5

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01HL153219
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS112363
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS111031
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS129804