Cryo-EM structure of the human TRPM4 channel in complex with EGTA and DAB at 37 degrees Celsius

Method: ELECTRON MICROSCOPY D_max: 168.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y2b
deposition_date	2025-08-31
title	Cryo-EM structure of the human TRPM4 channel in complex with EGTA and DAB at 37 degrees Celsius
keywords	ion channel, TRP channel, 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	53.37 Å
rg_electron	52.82 Å
i0	4657640000.00
molecular_weight	385690.0 kDa
excluded_volume	376640 Å³
envelope_volume	789540 Å³
shell_volume	121420 Å³
envelope_diameter	168.3 Å
shell_rg	59.88 Å
envelope_rg	50.55 Å
shape_rg	52.79 Å
total_rg	53.03 Å
total_atoms	29340
n_residues	3904
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	168.1 Å
rg_real	53.08 Å
rg_real_error	1.05 Å
i0_real	4.6580e+09
i0_real_error	9.3230e+07
rg_reciprocal	53.60 Å
i0_reciprocal	4661000000.0000
total_estimate	0.8775
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	69.5 Å
skewness	0.084
kurtosis	-0.473
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0001
highest_alpha	250400000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.791

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Transient receptor potential cation channel subfamily M member 4
formula_weight	134456.5 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	29340

MVVPEKEQSWIPKIFKKKTCTTFIVDSTDPGGTLCQCGRPRTAHPAVAMEDAFGAAVVTVWDSDAHTTEKPTDAYGELDFTGAGRKHSNFLRLSDRTDPAAVYSLVTRTWGFRAPNLVVSVLGGSGGPVLQTWLQDLLRRGLVRAAQSTGAWIVTGGLHTGIGRHVGVAVRDHQMASTGGTKVVAMGVAPWGVVRNRDTLINPKGSFPARYRWRGDPEDGVQFPLDYNYSAFFLVDDGTHGCLGGENRFRLRLESYISQQKTGVGGTGIDIPVLLLLIDGDEKMLTRIENATQAQLPCLLVAGSGGAADCLAETLEDTLAPGSGGARQGEARDRIRRFFPKGDLEVLQAQVERIMTRKELLTVYSSEDGSEEFETIVLKALVKACGSSEASAYLDELRLAVAWNRVDIAQSELFRGDIQWRSFHLEASLMDALLNDRPEFVRLLISHGLSLGHFLTPMRLAQLYSAAPSNSLIRNLLDQASHSAGTKAPALKGGAAELRPPDVGHVLRMLLGKMCAPRYPSGGAWDPHPGQGFGESMYLLSDKATSPLSLDAGLGQAPWSDLLLWALLLNRAQMAMYFWEMGSNAVSSALGACLLLRVMARLEPDAEEAARRKDLAFKFEGMGVDLFGECYRSSEVRAARLLLRRCPLWGDATCLQLAMQADARAFFAQDGVQSLLTQKWWGDMASTTPIWALVLAFFCPPLIYTRLITFRKSEEEPTREELEFDMDSVINGEGPVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHLRLLLRQLCRRPRSPQPSSPALEHFRVYLSKEAERKLLTWESVHKENFLLARARDKRESDSERLKRTSQKVDLALKQLGHIREYEQRLKVLEREVQQCSRVLGWVAEALSRSALLPPGGPPPPDLPGSKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	4,4'-[(pyridin-2-yl)methylene]diphenol
formula_weight	277.3 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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resolution	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	537300

fit	/app/data/saxs_computation/y2/9y2b/9y2b.fit
pddf	/app/data/pr_computation/y2/9y2b/9y2b.pr.out
profile	/app/data/saxs_computation/y2/9y2b/9y2b.dat