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- EMDB-71251: Zebrafish TRPM5 D797A mutant with 5mM calcium -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71251
TitleZebrafish TRPM5 D797A mutant with 5mM calcium
Map data
Sample
  • Complex: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium
    • 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 / calcium / CBTA / 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: Nat.Chem.Biol. / Year: 2026
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_71251.png

Downloads & links

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Map

FileDownload / File: emd_71251.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 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: 0.009
Minimum - Maximum-0.007735565 - 0.030891474
Average (Standard dev.)0.00035049272 (±0.0019512854)
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_71251_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_71251_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71251_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71251_half_map_2.map
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

EntireName: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium
Components
  • Complex: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium
    • 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

SupramoleculeName: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium
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: 122.298406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RLGDIDFTGV SRTRGKFVRV TSSTDPAEIY QILTKQWGLA PPHLVVALMG GDEVAQLKPW LRDTLRKGLV KAAQSTGAWI LTSGLRFGI TKNLGQAVRD HSLASTSPKV RVVAIGIAPW NMIQNRDLLL SAKPDHPATY PTEDLPYGAV YSLDCNHSHF I LVDEDPKR ...String:
RLGDIDFTGV SRTRGKFVRV TSSTDPAEIY QILTKQWGLA PPHLVVALMG GDEVAQLKPW LRDTLRKGLV KAAQSTGAWI LTSGLRFGI TKNLGQAVRD HSLASTSPKV RVVAIGIAPW NMIQNRDLLL SAKPDHPATY PTEDLPYGAV YSLDCNHSHF I LVDEDPKR PGATGEMRVK MLKHISLQRT GYGGTGSIEI PVLCLLVHGE PRILQKMYKN IQNSIPWLIL AGSGGVADIL VT LMDRGCW DADIVQELLI NTFPDGLHST EITSWTKLIQ RILDHGHLLT VHDPEQDSEL DTVILKALVK ACKSQSQEAQ DFL DELKLA VAWNRVDIAK SEIFSGDVQW SAQDLEEVMM EALVNDKPDF VRLFVDNGVN IKQFLTYGRL QELYCSVSEK NLLH TLLLK KNQERQAQLA RKRMSGNPNN ELGDRKFRFT FHEVSKVLKD FLDDTCKGFY QKLPAVSKAL HQKNLPDMDR RCEHP WRDL FLWAILQNRQ EMANYFWAMG PEAVAAALVG CKIMKEMAHL ATEAESARSM KNAKYEQFAM DLFSECYSNS EDRAYS LLV RKTCCWSKAT VLNIATLAEA KCFFAHDGVQ ALLTKVWWGA MRTDTSISRL VLTFFIPPLV WTSLIKFNPE EQVSKDE GE PFAELDSLET EQALLLTDGD PVAGEGSAET AARSCSATFI RVVLRRWNRF WSAPVTVFMG NVIMYFAFLI LFSYVLLL D FRPPPPYGPS AAEIILYFWV FTLVLEEIRQ SFFTDEDMSI LKKMKLYVED NWNKCAMVAI SLFVVGLSCR MAMSTYEAG RTVLALDFMV FTLRLIHIFA IHKQLGPKII IVERMIKDVF FFLFFLSVWL IAYGVTTQAL LHPNDPRIDW VFRRALYRPY LHIFGQIPL EEIDAAKMPD DNCTTDVQEI ILGTLPPCPN IYANWLVILL LVIYLLVTNV LLLNLLIAMF SYTFQVVQEN A DIFWKFQR YNLIVEYHSR PALAPPFIII SHITQALLSF IKKTENTQDL LERELPSGLD QKLMTWETVQ KENYLAKLEH EH RESSGER LRYTSSKVQT LLRMVGGFKD QEKRM

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: 96605
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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