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- EMDB-72694: Cryo-EM structure of wild-type human CNNM4 tetramer with Magnesiu... -

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Basic information

Entry
Database: EMDB / ID: EMD-72694
TitleCryo-EM structure of wild-type human CNNM4 tetramer with Magnesium and MgATP in outward-facing state
Map data
Sample
  • Complex: CNNM4/Mg/ATP tetramer
    • Protein or peptide: Metal transporter CNNM4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMagnesium transporter / membrane protein / transmembrane domain / ion binding / TRANSPORT PROTEIN
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
Metal transporter CNNM4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsBai Z / Zhou E / Lu W / Du J
Funding support United States, 4 items
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, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72694.png

Downloads & links

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Map

FileDownload / File: emd_72694.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 416 pix.
= 361.504 Å		0.87 Å/pix.
x 416 pix.
= 361.504 Å		0.87 Å/pix.
x 416 pix.
= 361.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.869 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00376
Minimum - Maximum-0.0035994654 - 0.019124037
Average (Standard dev.)0.00006816308 (±0.0004559933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 361.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_72694_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_72694_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72694_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : CNNM4/Mg/ATP tetramer

EntireName: CNNM4/Mg/ATP tetramer
Components
  • Complex: CNNM4/Mg/ATP tetramer
    • Protein or peptide: Metal transporter CNNM4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: CNNM4/Mg/ATP tetramer

SupramoleculeName: CNNM4/Mg/ATP tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Metal transporter CNNM4

MacromoleculeName: Metal transporter CNNM4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.140656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPVGGGGRP VGGPARGRLL LAAPVLLVLL WALGARGQGS PQQGTIVGMR LASCNKSCGT NPDGIIFVSE GSTVNLRLYG YSLGNISSN LISFTEVDDA ETLHKSTSCL ELTKDLVVQQ LVNVSRGNTS GVLVVLTKFL RRSESMKLYA LCTRAQPDGP W LKWTDKDS ...String:
MAPVGGGGRP VGGPARGRLL LAAPVLLVLL WALGARGQGS PQQGTIVGMR LASCNKSCGT NPDGIIFVSE GSTVNLRLYG YSLGNISSN LISFTEVDDA ETLHKSTSCL ELTKDLVVQQ LVNVSRGNTS GVLVVLTKFL RRSESMKLYA LCTRAQPDGP W LKWTDKDS LLFMVEEPGR FLPLWLHILL ITVLLVLSGI FSGLNLGLMA LDPMELRIVQ NCGTEKERRY ARKIEPIRRK GN YLLCSLL LGNVLVNTSL TILLDNLIGS GLMAVASSTI GIVIFGEILP QALCSRHGLA VGANTILLTK FFMLLTFPLS FPI SKLLDF FLGQEIRTVY NREKLMEMLK VTEPYNDLVK EELNMIQGAL ELRTKTVEDI MTQLQDCFMI RSDAILDFNT MSEI MESGY TRIPVFEDEQ SNIVDILYVK DLAFVDPDDC TPLKTITRFY NHPVHFVFHD TKLDAMLEEF KKGKSHLAIV QKVNN EGEG DPFYEVLGLV TLEDVIEEII KSEILDESDM YTDNRSRKRV SEKNKRDFSA FKDADNELKV KISPQLLLAA HRFLAT EVS QFSPSLISEK ILLRLLKYPD VIQELKFDEH NKYYARHYLY TRNKPADYFI LILQGKVEVE AGKENMKFET GAFSYYG TM ALTSVPSDRS PAHPTPLSRS ASLSYPDRTD VSTAATLAGS SNQFGSSVLG QYISDFSVRA LVDLQYIKIT RQQYQNGL L ASRMENSPQF PIDGCTTHME NLAEKSELPV VDETTTLLNE RNSLLHKASH ENAIVDGSLE VLFQGPSGGS RLEEELRRR LTEGGSWSHP QFEKGGGSGG GSGGSAWSHP QFEKGSHHHH HHHH

UniProtKB: Metal transporter CNNM4

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 16 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 6
Molecular weightTheoretical: 22.99 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 946137
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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