SAXSdb — 9qho

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1. Structure Basics

entry_id	9qho
deposition_date	2025-03-16
title	Cryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Primidone
keywords	Ca2+ channel Primidone-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	52.66 Å
rg_electron	52.27 Å
i0	2031690000.00
molecular_weight	403420.0 kDa
excluded_volume	515550 Å³
envelope_volume	814510 Å³
shell_volume	124920 Å³
envelope_diameter	162.5 Å
shell_rg	60.70 Å
envelope_rg	50.11 Å
shape_rg	52.38 Å
total_rg	52.15 Å
total_atoms	57304
n_residues	3432
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	158.0 Å
rg_real	52.35 Å
rg_real_error	0.86 Å
i0_real	2.0320e+09
i0_real_error	3.4120e+07
rg_reciprocal	52.90 Å
i0_reciprocal	2033000000.0000
total_estimate	0.8607
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	68.5 Å
skewness	0.073
kurtosis	-0.428
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	332300000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.484

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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	57304

MSGKKWRDAGELERGCSDREDSAESRRRSRSASRGRFAESWKRLSSKQGSTKRSGLPAQQTPAQKSWIERAFYKRECVHIIPSTKDPHRCCCGRLIGQHVGLTPSISVLQNEKNESRLSRNDIQSEKWSISKHTQLSPTDAFGTIEFQGGGHSNKAMYVRVSFDTKPDLLLHLMTKEWQLELPKLLISVHGGLQNFELQPKLKQVFGKGLIKAAMTTGAWIFTGGVNTGVIRHVGDALKDHASKSRGKICTIGIAPWGIVENQEDLIGRDVVRPYQTMSNPMSKLTVLNSMHSHFILADNGTTGKYGAEVKLRRQLEKHISLQKINTRIGQGVPVVALIVEGGPNVISIVLEYLRDTPPVPVVVCDGSGRASDILAFGHKYSEEGGLINESLRDQLLVTIQKTFTYTRTQAQHLFIILMECMKKKELITVFRMGSEGHQDIDLAILTALLKGANASAPDQLSLALAWNRVDIARSQIFIYGQQWPVGSLEQAMLDALVLDRVDFVKLLIENGVSMHRFLTISRLEELYNTRHGPSNTLYHLVRDVKKGNLPPDYRISLIDIGLVIEYLMGGAYRCNYTRKRFRTLYHNLFGPKRPKALKLLGMEDDIPLRRGRKTTKKREEEVDIDLDDPEINHFPFPFHELMVWAVLMKRQKMALFFWQHGEEAMAKALVACKLCKAMAHEASENDMVDDISQELNHNSRDFGQLAVELLDQSYKQDEQLAMKLLTYELKNWSNATCLQLAVAAKHRDFIAHTCSQMLLTDMWMGRLRMRKNSGLKVILGILLPPSILSLEFKNKDDMPYMTQAQEIHLQEKEPEEPEKPTKEKDEEDMELTAMLGRSNGESSRKKDEEEVQSRHRLIPVGRKIYEFYNAPIVKFWFYTLAYIGYLMLFNYIVLVKMERWPSTQEWIVISYIFTLGIEKMREILMSEPGKLLQKVKVWLQEYWNVTDLIAILLFSVGMILRLQDQPFRSDGRVIYCVNIIYWYIRLLDIFGVNKYLGPYVMMIGKMMIDMMYFVIIMLVVLMSFGVARQAILFPNEEPSWKLAKNIFYMPYWMIYGEVFADQIDPPCGQNETREDGKTIQLPPCKTGAWIVPAIMACYLLVANILLVNLLIAVFNNTFFEVKSISNQVWKFQRYQLIMTFHERPVLPPPLIIFSHMTMIFQHVCCRWRKHESDQDERDYGLKLFITDDELKKVHDFEEQCIEEYFREKDDRFNSSNDERIRVTSERVENMSMRLEEVNEREHSMKASLQTVDIRLAQLEDLIGRMATALERLTGLERAESNKIRSRTSSDCTDAAYIVRQSSFNSQEGNTFKLQESIDPAGEETISPTSPTLMPRMRSHSFYSVALEVLFQGPQGTEQKLISEEDLRGASMDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 non-polymer

description	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
formula_weight	544.8 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	primidone
formula_weight	218.3 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE
formula_weight	704.0 kDa
src_method	syn
entity_count	4

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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	3.280 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.28 Å
resolution_method	—
num_particles	76411

fit	/app/data/saxs_computation/qh/9qho/9qho.fit
pddf	/app/data/pr_computation/qh/9qho/9qho.pr.out
profile	/app/data/saxs_computation/qh/9qho/9qho.dat

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

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