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- EMDB-71249: Zebrafish TRPM5 with 2uM Ca in GDN detergent -

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Basic information

Entry
Database: EMDB / ID: EMD-71249
TitleZebrafish TRPM5 with 2uM Ca in GDN detergent
Map data
Sample
  • Complex: zebrafish TRPM5 in GDN detergent with 2uM calcium
    • Protein or peptide: Zebrafish TRPM5
KeywordsTRPM5 channel / ion channel / cation channel / sodium channel / calcium / CBTA / TRANSPORT PROTEIN
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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_71249.png

Downloads & links

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Map

FileDownload / File: emd_71249.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312.6 Å		1.04 Å/pix.
x 300 pix.
= 312.6 Å		1.04 Å/pix.
x 300 pix.
= 312.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.042 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.025851246 - 0.06023991
Average (Standard dev.)0.000047565234 (±0.0026062578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71249_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_71249_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71249_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_71249_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 in GDN detergent with 2uM calcium

EntireName: zebrafish TRPM5 in GDN detergent with 2uM calcium
Components
  • Complex: zebrafish TRPM5 in GDN detergent with 2uM calcium
    • Protein or peptide: Zebrafish TRPM5

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Supramolecule #1: zebrafish TRPM5 in GDN detergent with 2uM calcium

SupramoleculeName: zebrafish TRPM5 in GDN detergent with 2uM calcium / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: Zebrafish TRPM5

MacromoleculeName: Zebrafish TRPM5 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
SequenceString: MHHHHHHHHA AASAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGGSGGGS GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD ...String:
MHHHHHHHHA AASAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGGSGGGS GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNYNS HNVYIMADKQ KNGIKVNFKI RHNIEDGSVQ LADHYQQNTP IGDGPVLLPD NHYLSTQSKL SKDPNEKRDH MVLLEFVTAA GITLGMDELY KSGLRSGLVP RGSGGRATMV EKSSERFDKQ MAGRLGDIDF TGVSRTRGKF VRVTSSTDPA EIYQILTKQW GLAPPHLVVA LMGGDEVAQL KPWLRDTLRK GLVKAAQSTG AWILTSGLRF GITKNLGQAV RDHSLASTSP KVRVVAIGIA PWNMIQNRDL LLSAKPDHPA TYPTEDLPYG AVYSLDCNHS HFILVDEDPK RPGATGEMRV KMLKHISLQR TGYGGTGSIE IPVLCLLVHG EPRILQKMYK NIQNSIPWLI LAGSGGVADI LVTLMDRGCW DADIVQELLI NTFPDGLHST EITSWTKLIQ RILDHGHLLT VHDPEQDSEL DTVILKALVK ACKSQSQEAQ DFLDELKLAV AWNRVDIAKS EIFSGDVQWS AQDLEEVMME ALVNDKPDFV RLFVDNGVNI KQFLTYGRLQ ELYCSVSEKN LLHTLLLKKN QERQAQLARK RMSGNPNNEL GDRKFRFTFH EVSKVLKDFL DDTCKGFYQK LPAERMGKGR LFHSQKNLPD MDRRCEHPWR DLFLWAILQN RQEMANYFWA MGPEAVAAAL VGCKIMKEMA HLATEAESAR SMKNAKYEQF AMDLFSECYS NSEDRAYSLL VRKTCCWSKA TVLNIATLAE AKCFFAHDGV QALLTKVWWG AMRTDTSISR LVLTFFIPPL VWTSLIKFNP EEQVSKDEGE PFAELDSLET EQALLLTDGD PVAGEGSAET AARSCSATFI RVVLRRWNRF WSAPVTVFMG NVIMYFAFLI LFSYVLLLDF RPPPPYGPSA AEIILYFWVF TLVLEEIRQS FFTDEDMSIL KKMKLYVEDN WNKCDMVAIS LFVVGLSCRM AMSTYEAGRT VLALDFMVFT LRLIHIFAIH KQLGPKIIIV ERMIKDVFFF LFFLSVWLIA YGVTTQALLH PNDPRIDWVF RRALYRPYLH IFGQIPLEEI DAAKMPDDNC TTDVQEIILG TLPPCPNIYA NWLVILLLVI YLLVTNVLLL NLLIAMFSYT FQVVQENADI FWKFQRYNLI VEYHSRPALA PPFIIISHIT QALLSFIKKT ENTQDLLERE LPSGLDQKLM TWETVQKENY LAKLEHEHRE SSGERLRYTS SKVQTLLRMV GGFKDQEKRM ATVETEVRYC GEVLSWIAEC FHKSTLKCDR DAPKAPRSIA GSSRDQQPQG AKRQQPGGHP AYGTDKKLPF IDHFE

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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 K2 SUMMIT (4k 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42900
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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