SAXSdb — 9vql

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1. Structure Basics

entry_id	9vql
deposition_date	2025-07-05
title	Cryo-EM structure of the dimeric Elapor1 mutant
keywords	Tethering factor, 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	48.08 Å
rg_electron	47.58 Å
i0	468531000.00
molecular_weight	173060.0 kDa
excluded_volume	213530 Å³
envelope_volume	322670 Å³
shell_volume	56537 Å³
envelope_diameter	154.9 Å
shell_rg	51.64 Å
envelope_rg	46.46 Å
shape_rg	47.54 Å
total_rg	47.89 Å
total_atoms	12122
n_residues	1626
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	152.8 Å
rg_real	48.03 Å
rg_real_error	1.37 Å
i0_real	4.6850e+08
i0_real_error	9.1300e+06
rg_reciprocal	48.08 Å
i0_reciprocal	468600000.0000
total_estimate	0.8872
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.6 Å
skewness	0.165
kurtosis	-0.692
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	25490000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.624

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Endosome/lysosome-associated apoptosis and autophagy regulator 1
formula_weight	110429.4 kDa
mutation	T42M/H47A/H55A/H74A/H309A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12122

MKTIIALSYIFCLVFADYKDDDDKGSHHHHHHSGMGPELAACKESEYAFEYTACDSTGSRWRVAVPASPGLCTSLPDPVKGTECSFSCNAGEFLDMKDQSCKPCAEGRYSLGTGIRFDEWDELPHGFASLSANLEVDDSISESTENCTSSKWVPRGDYIASNTDECTATLMYAVNLKQSGTVNFEYYYPDSSIIFEFFVQNDQCQPSADDSRWMKTTEKGWEFHSVELNRGNNVLYWRTTAFSVWSKVSKPVLVRNIAITGVAYTSECFPCKPGTYAAKQGSPFCKLCPANYYSNKGETSCAPCDADKYSEKGSSTCKVRPACTDKDYFYTHTACDAQGETQLMYKWAIPKICGEDLEGAVKLPASGVKTRCPPCNPGFFKTDNSTCEPCPYGSYSNGSDCTHCPAGTEPAVGFEYKWWNTLPSNMETTVLSGINFEYKGLTGWEVAGDHIYTAVGASDNDFMILTLVVPGFRPPQSVVADTENKEVARITFVFETICSVNCELYFMVGMNSRTNTPVETWKGTKGKQSYTYTIEENATVSFTWAFQRTTLHETGRKYTNDVAKIYSINVTNVMGGVASYCRPCALEASDLGSSCTSCPAGHYINRDSGTCHLCPSNTILKAHQPYGAQACVPCGPGTKNNKIHSLCYNDCTFSRNTPSRIFNYNFSALAGTVSLAGVPSFTSKGLKYFHHFTLSLCGNQGKKMAVCTDNVTDLRIPDGEAGFSKSVTAYVCQVVIIPSEVMGYKAGVSSQPVSLADRLVGVSTDMTLEGIVSPVELFHPETSGIPDIVFFFRSNDVTQSCSSGRSTTIRLRCNPMKAAPGTLRLPSMCSDGTCDGCNFHFLWESVAACPLCSASDYHTFVSSCVAGIQKTTYMWREPKLCSGGISLPEQRVTICKTIDFWLKVGISAGTCTAILLTVLTCYFWKKNQKLEYKYSKLVMNATLKDCDLPAADSCAIMEGEDVEDDFIFTSKKSLFGKIKSFTSKRTPDGFDSVPLKTSSGGPDMDM

Source

organism	Mus musculus
common_name	mice
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	4

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	6

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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	3.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.60 Å
resolution_method	—
num_particles	196230

fit	/app/data/saxs_computation/vq/9vql/9vql.fit
pddf	/app/data/pr_computation/vq/9vql/9vql.pr.out
profile	/app/data/saxs_computation/vq/9vql/9vql.dat

Cryo-EM structure of the dimeric Elapor1 mutant

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