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- EMDB-71245: The open state of zebrafish TRPM5 with 1mM EDTA and 0.5mM CBTA -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71245
TitleThe open state of zebrafish TRPM5 with 1mM EDTA and 0.5mM CBTA
Map data
Sample
  • Complex: Open state of zebrafish TRPM5 in GDN detergent with 1mM EDTA and 0.5mM CBTA
    • Protein or peptide: Green fluorescent protein,Transient receptor potential cation channel subfamily M member 5
  • Ligand: CALCIUM ION
  • Ligand: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
  • Ligand: (25R)-14beta,17beta-spirost-5-en-3beta-ol
  • Ligand: 5-chloro-N-[(5-chloro-1,3-thiazol-2-yl)methyl]-1,2-benzothiazol-6-amine
KeywordsTRPM5 channel / ion channel / cation channel / sodium channel / calcium / CBTA / TRANSPORT PROTEIN
Function / homology
Function and homology information


calcium-activated cation channel activity / bioluminescence / generation of precursor metabolites and energy / calcium channel activity / calcium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Green fluorescent protein / 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_71245.png

Downloads & links

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Map

FileDownload / File: emd_71245.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-0.021936424 - 0.043808658
Average (Standard dev.)0.000024261395 (±0.0020857656)
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_71245_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_71245_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71245_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_71245_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 : Open state of zebrafish TRPM5 in GDN detergent with 1mM EDTA and ...

EntireName: Open state of zebrafish TRPM5 in GDN detergent with 1mM EDTA and 0.5mM CBTA
Components
  • Complex: Open state of zebrafish TRPM5 in GDN detergent with 1mM EDTA and 0.5mM CBTA
    • Protein or peptide: Green fluorescent protein,Transient receptor potential cation channel subfamily M member 5
  • Ligand: CALCIUM ION
  • Ligand: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
  • Ligand: (25R)-14beta,17beta-spirost-5-en-3beta-ol
  • Ligand: 5-chloro-N-[(5-chloro-1,3-thiazol-2-yl)methyl]-1,2-benzothiazol-6-amine

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Supramolecule #1: Open state of zebrafish TRPM5 in GDN detergent with 1mM EDTA and ...

SupramoleculeName: Open state of zebrafish TRPM5 in GDN detergent with 1mM EDTA and 0.5mM CBTA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: Green fluorescent protein,Transient receptor potential cation cha...

MacromoleculeName: Green fluorescent protein,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: 166.815672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHA AASAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGGSGGGS GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGD ATYGKLTLKF ICTTGKLPVP WPTLVTTLTY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY K TRAEVKFE ...String:
MHHHHHHHHA AASAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGGSGGGS GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGD ATYGKLTLKF ICTTGKLPVP WPTLVTTLTY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY K TRAEVKFE GDTLVNRIEL KGIDFKEDGN ILGHKLEYNY NSHNVYIMAD KQKNGIKVNF KIRHNIEDGS VQLADHYQQN TP IGDGPVL LPDNHYLSTQ SKLSKDPNEK RDHMVLLEFV TAAGITLGMD ELYKSGLRSG LVPRGSGGRA TMVEKSSERF DKQ MAGRLG DIDFTGVSRT RGKFVRVTSS TDPAEIYQIL TKQWGLAPPH LVVALMGGDE VAQLKPWLRD TLRKGLVKAA QSTG AWILT SGLRFGITKN LGQAVRDHSL ASTSPKVRVV AIGIAPWNMI QNRDLLLSAK PDHPATYPTE DLPYGAVYSL DCNHS HFIL VDEDPKRPGA TGEMRVKMLK HISLQRTGYG GTGSIEIPVL CLLVHGEPRI LQKMYKNIQN SIPWLILAGS GGVADI LVT LMDRGCWDAD IVQELLINTF PDGLHSTEIT SWTKLIQRIL DHGHLLTVHD PEQDSELDTV ILKALVKACK SQSQEAQ DF LDELKLAVAW NRVDIAKSEI FSGDVQWSAQ DLEEVMMEAL VNDKPDFVRL FVDNGVNIKQ FLTYGRLQEL YCSVSEKN L LHTLLLKKNQ ERQAQLARKR MSGNPNNELG DRKFRFTFHE VSKVLKDFLD DTCKGFYQKL PAERMGKGRL FHSQKNLPD MDRRCEHPWR DLFLWAILQN RQEMANYFWA MGPEAVAAAL VGCKIMKEMA HLATEAESAR SMKNAKYEQF AMDLFSECYS NSEDRAYSL LVRKTCCWSK ATVLNIATLA EAKCFFAHDG VQALLTKVWW GAMRTDTSIS RLVLTFFIPP LVWTSLIKFN P EEQVSKDE GEPFAELDSL ETEQALLLTD GDPVAGEGSA ETAARSCSAT FIRVVLRRWN RFWSAPVTVF MGNVIMYFAF LI LFSYVLL LDFRPPPPYG PSAAEIILYF WVFTLVLEEI RQSFFTDEDM SILKKMKLYV EDNWNKCDMV AISLFVVGLS CRM AMSTYE AGRTVLALDF MVFTLRLIHI FAIHKQLGPK IIIVERMIKD VFFFLFFLSV WLIAYGVTTQ ALLHPNDPRI DWVF RRALY RPYLHIFGQI PLEEIDAAKM PDDNCTTDVQ EIILGTLPPC PNIYANWLVI LLLVIYLLVT NVLLLNLLIA MFSYT FQVV QENADIFWKF QRYNLIVEYH SRPALAPPFI IISHITQALL SFIKKTENTQ DLLERELPSG LDQKLMTWET VQKENY LAK LEHEHRESSG ERLRYTSSKV QTLLRMVGGF KDQEKRMATV ETEVRYCGEV LSWIAECFHK STLKCDRDAP KAPRSIA GS SRDQQPQGAK RQQPGGHPAY GTDKKLPFID HFE

UniProtKB: Green fluorescent protein, Transient receptor potential cation channel subfamily M member 5

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-...

MacromoleculeName: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
type: ligand / ID: 3 / Number of copies: 4 / Formula: YUY
Molecular weightTheoretical: 841.033 Da
Chemical component information

ChemComp-YUY:
(2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside

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Macromolecule #4: (25R)-14beta,17beta-spirost-5-en-3beta-ol

MacromoleculeName: (25R)-14beta,17beta-spirost-5-en-3beta-ol / type: ligand / ID: 4 / Number of copies: 4 / Formula: YUV
Molecular weightTheoretical: 414.621 Da
Chemical component information

ChemComp-YUV:
(25R)-14beta,17beta-spirost-5-en-3beta-ol

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Macromolecule #5: 5-chloro-N-[(5-chloro-1,3-thiazol-2-yl)methyl]-1,2-benzothiazol-6...

MacromoleculeName: 5-chloro-N-[(5-chloro-1,3-thiazol-2-yl)methyl]-1,2-benzothiazol-6-amine
type: ligand / ID: 5 / Number of copies: 4 / Formula: A1CGW
Molecular weightTheoretical: 316.229 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: 200 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: 5426
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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