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9t9u

Cryo-EM composite structure of mouse TRPM3 alpha 2 in complex with antagonist Ononetin

Method: ELECTRON MICROSCOPY D_max: 164.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t9u
deposition_date	2025-11-17
title	Cryo-EM composite structure of mouse TRPM3 alpha 2 in complex with antagonist Ononetin
keywords	Ca2+ channel Ononetin-bound Closed conformation, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	54.41 Å
rg_electron	54.02 Å
i0	2885630000.00
molecular_weight	479120.0 kDa
excluded_volume	610850 Å³
envelope_volume	927240 Å³
shell_volume	137060 Å³
envelope_diameter	166.7 Å
shell_rg	63.01 Å
envelope_rg	51.75 Å
shape_rg	54.06 Å
total_rg	54.11 Å
total_atoms	67940
n_residues	4104
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	164.8 Å
rg_real	54.06 Å
rg_real_error	0.88 Å
i0_real	2.8860e+09
i0_real_error	4.8890e+07
rg_reciprocal	54.69 Å
i0_reciprocal	2888000000.0000
total_estimate	0.6407
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	73.9 Å
skewness	0.049
kurtosis	-0.477
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	387800000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 0.017; Positv: 1.000; Valcen: 0.935; Smooth: 0.596

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	MKIAA1616 protein
formula_weight	161963.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	67940

MSGKKWRDAGELERGCSDREDSAESRRRSRSASRGRFAESWKRLSSKQGSTKRSGLPAQQTPAQKSWIERAFYKRECVHIIPSTKDPHRCCCGRLIGQHVGLTPSISVLQNEKNESRLSRNDIQSEKWSISKHTQLSPTDAFGTIEFQGGGHSNKAMYVRVSFDTKPDLLLHLMTKEWQLELPKLLISVHGGLQNFELQPKLKQVFGKGLIKAAMTTGAWIFTGGVNTGVIRHVGDALKDHASKSRGKICTIGIAPWGIVENQEDLIGRDVVRPYQTMSNPMSKLTVLNSMHSHFILADNGTTGKYGAEVKLRRQLEKHISLQKINTRIGQGVPVVALIVEGGPNVISIVLEYLRDTPPVPVVVCDGSGRASDILAFGHKYSEEGGLINESLRDQLLVTIQKTFTYTRTQAQHLFIILMECMKKKELITVFRMGSEGHQDIDLAILTALLKGANASAPDQLSLALAWNRVDIARSQIFIYGQQWPVGSLEQAMLDALVLDRVDFVKLLIENGVSMHRFLTISRLEELYNTRHGPSNTLYHLVRDVKKGNLPPDYRISLIDIGLVIEYLMGGAYRCNYTRKRFRTLYHNLFGPKRPKALKLLGMEDDIPLRRGRKTTKKREEEVDIDLDDPEINHFPFPFHELMVWAVLMKRQKMALFFWQHGEEAMAKALVACKLCKAMAHEASENDMVDDISQELNHNSRDFGQLAVELLDQSYKQDEQLAMKLLTYELKNWSNATCLQLAVAAKHRDFIAHTCSQMLLTDMWMGRLRMRKNSGLKVILGILLPPSILSLEFKNKDDMPYMTQAQEIHLQEKEPEEPEKPTKEKDEEDMELTAMLGRSNGESSRKKDEEEVQSRHRLIPVGRKIYEFYNAPIVKFWFYTLAYIGYLMLFNYIVLVKMERWPSTQEWIVISYIFTLGIEKMREILMSEPGKLLQKVKVWLQEYWNVTDLIAILLFSVGMILRLQDQPFRSDGRVIYCVNIIYWYIRLLDIFGVNKYLGPYVMMIGKMMIDMMYFVIIMLVVLMSFGVARQAILFPNEEPSWKLAKNIFYMPYWMIYGEVFADQIDPPCGQNETREDGKTIQLPPCKTGAWIVPAIMACYLLVANILLVNLLIAVFNNTFFEVKSISNQVWKFQRYQLIMTFHERPVLPPPLIIFSHMTMIFQHVCCRWRKHESDQDERDYGLKLFITDDELKKVHDFEEQCIEEYFREKDDRFNSSNDERIRVTSERVENMSMRLEEVNEREHSMKASLQTVDIRLAQLEDLIGRMATALERLTGLERAESNKIRSRTSSDCTDAAYIVRQSSFNSQEGNTFKLQESIDPAGEETISPTSPTLMPRMRSHSFYSVALEVLFQGPQGTEQKLISEEDLRGASMDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 non-polymer

description	1-[2,4-bis(oxidanyl)phenyl]-2-(4-methoxyphenyl)ethanone
formula_weight	258.3 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
formula_weight	705.0 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	(25R)-14beta,17beta-spirost-5-en-3beta-ol
formula_weight	414.6 kDa
src_method	syn
entity_count	8

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.610 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.61 Å
resolution_method	—
num_particles	309057

fit	/app/data/saxs_computation/t9/9t9u/9t9u.fit
pddf	/app/data/pr_computation/t9/9t9u/9t9u.pr.out
profile	/app/data/saxs_computation/t9/9t9u/9t9u.dat

Cryo-EM composite structure of mouse TRPM3 alpha 2 in complex with antagonist Ononetin

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D