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- EMDB-71257: Zebrafish TRPM5 Q771A mutant with 5mM calcium -

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Basic information

Entry
Database: EMDB / ID: EMD-71257
TitleZebrafish TRPM5 Q771A mutant with 5mM calcium
Map dataZebrafish TRPM5 Q771A mutant with 5mM calcium
Sample
  • Complex: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium
    • Protein or peptide: RNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: (10xi,22xi,25R)-5beta,13xi,14beta,17beta-spirostan-3beta-ol
  • Ligand: (2R)-2-(hydroxymethyl)-4-{[(10xi,13xi,22xi,25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
KeywordsTRPM5 channel / ion channel / cation channel / sodium channel / TRANSPORT PROTEIN / TRANSFERASE
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / calcium-activated cation channel activity / bioluminescence / generation of precursor metabolites and energy / virion component / calcium channel activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / calcium-activated cation channel activity / bioluminescence / generation of precursor metabolites and energy / virion component / calcium channel activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / calcium ion binding / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / RNA-directed RNA polymerase, paramyxovirus / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Transient receptor potential channel, canonical / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase ...RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / RNA-directed RNA polymerase, paramyxovirus / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Transient receptor potential channel, canonical / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / 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
RNA-directed RNA polymerase L / Transient receptor potential cation channel subfamily M member 5
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 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_71257.png

Downloads & links

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Map

FileDownload / File: emd_71257.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationZebrafish TRPM5 Q771A mutant with 5mM calcium
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: 0.0035
Minimum - Maximum-0.004432049 - 0.01645685
Average (Standard dev.)0.00010640855 (±0.0007780486)
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_71257_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: Additional Map

Fileemd_71257_additional_1.map
AnnotationAdditional Map
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Additional map: subunit class 6

Fileemd_71257_additional_2.map
Annotationsubunit class 6
Projections & Slices
AxesZYX

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Additional map: subunit class 5

Fileemd_71257_additional_3.map
Annotationsubunit class 5
Projections & Slices
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Additional map: subunit class 4

Fileemd_71257_additional_4.map
Annotationsubunit class 4
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Additional map: subunit class 3

Fileemd_71257_additional_5.map
Annotationsubunit class 3
Projections & Slices
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Additional map: subunit class 2

Fileemd_71257_additional_6.map
Annotationsubunit class 2
Projections & Slices
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Histogram

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Additional map: subunit class 1

Fileemd_71257_additional_7.map
Annotationsubunit class 1
Projections & Slices
AxesZYX

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Histogram

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Half map: Half Map B

Fileemd_71257_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Half map: Half Map A

Fileemd_71257_half_map_2.map
AnnotationHalf Map A
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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: RNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: (10xi,22xi,25R)-5beta,13xi,14beta,17beta-spirostan-3beta-ol
  • Ligand: (2R)-2-(hydroxymethyl)-4-{[(10xi,13xi,22xi,25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside

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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: RNA-directed RNA polymerase L,Transient receptor potential cation...

MacromoleculeName: RNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: NNS virus cap methyltransferase
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 166.758625 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 RASFFTDEDM 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: RNA-directed RNA polymerase L, 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: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: (10xi,22xi,25R)-5beta,13xi,14beta,17beta-spirostan-3beta-ol

MacromoleculeName: (10xi,22xi,25R)-5beta,13xi,14beta,17beta-spirostan-3beta-ol
type: ligand / ID: 4 / Number of copies: 4 / Formula: A1CGZ
Molecular weightTheoretical: 416.636 Da

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Macromolecule #5: (2R)-2-(hydroxymethyl)-4-{[(10xi,13xi,22xi,25R)-5beta,14beta,17be...

MacromoleculeName: (2R)-2-(hydroxymethyl)-4-{[(10xi,13xi,22xi,25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
type: ligand / ID: 5 / Number of copies: 4 / Formula: A1CG0
Molecular weightTheoretical: 843.049 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: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 3662754
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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