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- PDB-9y9f: Cryo-EM structure of human CNNM4(D262C) tetramer with Magnesium a... -

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Basic information

Entry
Database: PDB / ID: 9y9f
TitleCryo-EM structure of human CNNM4(D262C) tetramer with Magnesium and MgATP in occluded state
ComponentsMetal transporter CNNM4
KeywordsTRANSPORT PROTEIN / Magnesium transporter / membrane protein / transmembrane domain / ion binding
Function / homology
Function and homology information


sodium ion transmembrane transporter activity / biomineral tissue development / magnesium ion transport / magnesium ion homeostasis / intracellular monoatomic cation homeostasis / magnesium ion transmembrane transporter activity / visual perception / basolateral plasma membrane / protein-containing complex / plasma membrane
Similarity search - Function
: / Metal transporter CNNM4-like, immunoglobulin-like domain / Metal transporter CNNM2-like, C-terminal CNBH domain / Ancient conserved domain protein family / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / CBS domain superfamily / CBS domain ...: / Metal transporter CNNM4-like, immunoglobulin-like domain / Metal transporter CNNM2-like, C-terminal CNBH domain / Ancient conserved domain protein family / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Metal transporter CNNM4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsBai, Z. / Zhou, E. / Lu, W. / Du, J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL153219 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS112363 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS111031 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS129804 United States
CitationJournal: To Be Published
Title: Dynamic dimer-of-dimers architecture defines Mg2+ transport in human CNNM4
Authors: Bai, Z. / Zhou, E. / Lu, W. / Du, J.
History
DepositionSep 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Metal transporter CNNM4
B: Metal transporter CNNM4
C: Metal transporter CNNM4
D: Metal transporter CNNM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,93224
Polymers376,5154
Non-polymers2,41820
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Metal transporter CNNM4 / Ancient conserved domain-containing protein 4 / Cyclin-M4


Mass: 94128.711 Da / Num. of mol.: 4 / Mutation: D262C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM4, ACDP4, KIAA1592 / Cell line (production host): TSA201 / Production host: Homo sapiens (human) / References: UniProt: Q6P4Q7
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CNNM4(D262C)/Mg/ATP tetramer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: TSA201
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.21.2_5419model refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124298 / Symmetry type: POINT
RefinementHighest resolution: 3.69 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00420860
ELECTRON MICROSCOPYf_angle_d0.49428218
ELECTRON MICROSCOPYf_dihedral_angle_d9.9187934
ELECTRON MICROSCOPYf_chiral_restr0.0413296
ELECTRON MICROSCOPYf_plane_restr0.0033538

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