SAXSdb — 9vfi

▼

1. Structure Basics

entry_id	9vfi
deposition_date	2025-06-11
title	Structure of hTRPC3 solubilized with 4F peptide at 2.72 angstrom
keywords	TRPC3, 4F peptide, native lipid environment, METAL TRANSPORT; METAL TRANSPORT
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	46.15 Å
rg_electron	45.62 Å
i0	2879560000.00
molecular_weight	306110.0 kDa
excluded_volume	301310 Å³
envelope_volume	559560 Å³
shell_volume	98729 Å³
envelope_diameter	154.5 Å
shell_rg	53.38 Å
envelope_rg	44.59 Å
shape_rg	45.62 Å
total_rg	45.83 Å
total_atoms	23216
n_residues	2884
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

▼

3. P(r) Analysis (GNOM)

dmax	147.5 Å
rg_real	45.90 Å
rg_real_error	0.89 Å
i0_real	2.8800e+09
i0_real_error	4.4990e+07
rg_reciprocal	46.15 Å
i0_reciprocal	2880000000.0000
total_estimate	0.8702
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	60.7 Å
skewness	0.201
kurtosis	-0.304
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	137700000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.808

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	;Green fluorescence protein,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3,Maltose/maltodextrin-binding periplasmic protein,Short transient receptor potential channel 3 ;
formula_weight	173360.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	23248

MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATIGKLTLKFISTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGKYKTRAVVKFEGDTLVNRIELKGTDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFTVRHNVEGSGHHHHHHHHHHHHSSGLVPRGSGWSHPQFEKGSGDYKDDDDKGSGWSHPQFEKGSGDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQTVLSKDPNEKRDHMVLLEFVTAAGITHGMDELYKGSMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTGGLEVLFQGPEFGLNDIFEAQKIEWHEGSGSGSMREKGRRQAVRGPAFMFNDRGTSLTAEEERFLDAAEYGNIPVVRKMLEESKTLNVNCVDYMGQNALQLAVGNEHLEVTELLLKKENLARIGDALLLAISKGYVRIVEAILNHPGFAASKRLTLSPCEQELQDDDFYAYDEDGTRFSPDITPIILAAHCQKYEVVHMLLMKGARIERPHDYFCKCGDCMEKQRHDSFSHSRSRINAYKGLASPAYLSLSSEDPVLTALELSNELAKLANIEKEFKNDYRKLSMQCKDFVVGVLDLCRDSEEVEAILNGDLESAEPLEVHRHKASLSRVKLAIKYEVKKFVAHPNCQQQLLTIWYENLSGLREQTIAIKCLVVLVVALGLPFLAIGYWIAPCSRLGKILRSPFMKFVAHAASFIIFLGLLVFNASDRFEGITTLPNITVTDYPKQIFRVKTTQFTWTEMLIMVWVLGMMWSECKELWLEGPREYILQLWNVLDFGMLSIFIAAFTARFLAFLQATKAQQYVDSYVQESDLSEVTLPPEIQYFTYARDKWLPSDPQIISEGLYAIAVVLSFSRIAYILPANESFGPLQISLGRTVKDIFKFMVLFIMVFFAFMIGMFILYSYYLGAKVNAAFTTVEESFKTLFWSIFGLSEVTSVVLKYDHKFIENIGYVLYGIYNVTMVVVLLNMLIAMINSSYQEIEDDSDVEWKFARSKLWLSYFDDGKTLPPPFSLVPSPKSFVYFIMRIVNFPKCRRRRLQKDIEMGMGNSKSRLNLFTQSNSRVFESHSFNSILNQPTRYQQIMKRLIKRYVLKAQVDKENDEVNEGELKEIKQDISSLRYELLEDKSQATEELAILIHKLSEKLNPSMLRCE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	[(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
formula_weight	621.0 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	32

▶

6. Citations (1)

▶

resolution	2.72 Å
resolution_method	—
num_particles	65480

fit	/app/data/saxs_computation/vf/9vfi/9vfi.fit
pddf	/app/data/pr_computation/vf/9vfi/9vfi.pr.out
profile	/app/data/saxs_computation/vf/9vfi/9vfi.dat

Structure of hTRPC3 solubilized with 4F peptide at 2.72 angstrom

SAXS Profile

P(r) Distribution