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- EMDB-71252: Zebrafish TRPM5 D797A mutant with 5mM calcium and 0.5mM CBTA -

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Basic information

Entry
Database: EMDB / ID: EMD-71252
TitleZebrafish TRPM5 D797A mutant with 5mM calcium and 0.5mM CBTA
Map dataZebrafish TRPM5 D797A mutant with 5mM calcium and 0.5mM CBTA
Sample
  • Complex: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium anbd 0.5mM CBTA
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsTRPM5 channel / ion channel / cation channel / sodium channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


calcium channel activity / membrane
Similarity search - Function
: / Transient receptor potential channel, canonical / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 5
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRuan Z / Du J / Lu W
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R00NS128258 United States
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 General Medical Sciences (NIH/NIGMS)R35GM138321 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: A single allosteric site merges activation, modulation and inhibition in TRPM5
Authors: Ruan Z / Du J / Lu W
History
DepositionJun 14, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71252.png

Downloads & links

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Map

FileDownload / File: emd_71252.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationZebrafish TRPM5 D797A mutant with 5mM calcium and 0.5mM CBTA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00243
Minimum - Maximum-0.0052294014 - 0.01204699
Average (Standard dev.)0.00005037368 (±0.0005428544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71252_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map

Fileemd_71252_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_71252_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_71252_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium an...

EntireName: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium anbd 0.5mM CBTA
Components
  • Complex: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium anbd 0.5mM CBTA
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium an...

SupramoleculeName: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium anbd 0.5mM CBTA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: Transient receptor potential cation channel subfamily M member 5

MacromoleculeName: Transient receptor potential cation channel subfamily M member 5
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 132.103281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVEKSSERFD KQMAGRLGDI DFTGVSRTRG KFVRVTSSTD PAEIYQILTK QWGLAPPHLV VALMGGDEVA QLKPWLRDTL RKGLVKAAQ STGAWILTSG LRFGITKNLG QAVRDHSLAS TSPKVRVVAI GIAPWNMIQN RDLLLSAKPD HPATYPTEDL P YGAVYSLD ...String:
MVEKSSERFD KQMAGRLGDI DFTGVSRTRG KFVRVTSSTD PAEIYQILTK QWGLAPPHLV VALMGGDEVA QLKPWLRDTL RKGLVKAAQ STGAWILTSG LRFGITKNLG QAVRDHSLAS TSPKVRVVAI GIAPWNMIQN RDLLLSAKPD HPATYPTEDL P YGAVYSLD CNHSHFILVD EDPKRPGATG EMRVKMLKHI SLQRTGYGGT GSIEIPVLCL LVHGEPRILQ KMYKNIQNSI PW LILAGSG GVADILVTLM DRGCWDADIV QELLINTFPD GLHSTEITSW TKLIQRILDH GHLLTVHDPE QDSELDTVIL KAL VKACKS QSQEAQDFLD ELKLAVAWNR VDIAKSEIFS GDVQWSAQDL EEVMMEALVN DKPDFVRLFV DNGVNIKQFL TYGR LQELY CSVSEKNLLH TLLLKKNQER QAQLARKRMS GNPNNELGDR KFRFTFHEVS KVLKDFLDDT CKGFYQKLPA VSKAL HQKN LPDMDRRCEH PWRDLFLWAI LQNRQEMANY FWAMGPEAVA AALVGCKIMK EMAHLATEAE SARSMKNAKY EQFAMD LFS ECYSNSEDRA YSLLVRKTCC WSKATVLNIA TLAEAKCFFA HDGVQALLTK VWWGAMRTDT SISRLVLTFF IPPLVWT SL IKFNPEEQVS KDEGEPFAEL DSLETEQALL LTDGDPVAGE GSAETAARSC SATFIRVVLR RWNRFWSAPV TVFMGNVI M YFAFLILFSY VLLLDFRPPP PYGPSAAEII LYFWVFTLVL EEIRQSFFTD EDMSILKKMK LYVEDNWNKC AMVAISLFV VGLSCRMAMS TYEAGRTVLA LDFMVFTLRL IHIFAIHKQL GPKIIIVERM IKDVFFFLFF LSVWLIAYGV TTQALLHPND PRIDWVFRR ALYRPYLHIF GQIPLEEIDA AKMPDDNCTT DVQEIILGTL PPCPNIYANW LVILLLVIYL LVTNVLLLNL L IAMFSYTF QVVQENADIF WKFQRYNLIV EYHSRPALAP PFIIISHITQ ALLSFIKKTE NTQDLLEREL PSGLDQKLMT WE TVQKENY LAKLEHEHRE SSGERLRYTS SKVQTLLRMV GGFKDQEKRM ATVETEVRYC GEVLSWIAEC FHKSTLKCDR DAP KAPRSI AGSSRDQQPQ GAKRQQPAGH PAYGTDKKLP FIDH

UniProtKB: Transient receptor potential cation channel subfamily M member 5

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21138
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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