SAXSdb — 9vqm

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1. Structure Basics

entry_id	9vqm
deposition_date	2025-07-05
title	Cryo-EM structure of Elapor1WT in tetrameric form
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	74.39 Å
rg_electron	74.75 Å
i0	1849000000.00
molecular_weight	350800.0 kDa
excluded_volume	433130 Å³
envelope_volume	775620 Å³
shell_volume	90116 Å³
envelope_diameter	273.3 Å
shell_rg	66.15 Å
envelope_rg	72.56 Å
shape_rg	74.68 Å
total_rg	74.85 Å
total_atoms	24538
n_residues	3162
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	267.9 Å
rg_real	74.67 Å
rg_real_error	3.79 Å
i0_real	1.8490e+09
i0_real_error	4.7210e+07
rg_reciprocal	73.16 Å
i0_reciprocal	1843000000.0000
total_estimate	0.8477
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	89.3 Å
skewness	0.330
kurtosis	-0.615
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.0003
highest_alpha	65160000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.649

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Endosome/lysosome-associated apoptosis and autophagy regulator 1
formula_weight	108851.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	24538

DYKDDDDKGSHHHHHHSGTGPELHACKESEYHFEYTACDSTGSRWRVAVPHSPGLCTSLPDPVKGTECSFSCNAGEFLDMKDQSCKPCAEGRYSLGTGIRFDEWDELPHGFASLSANLEVDDSISESTENCTSSKWVPRGDYIASNTDECTATLMYAVNLKQSGTVNFEYYYPDSSIIFEFFVQNDQCQPSADDSRWMKTTEKGWEFHSVELNRGNNVLYWRTTAFSVWSKVSKPVLVRNIAITGVAYTSECFPCKPGTYAAKQGSPFCKLCPANYYSNKGETSCHPCDADKYSEKGSSTCKVRPACTDKDYFYTHTACDAQGETQLMYKWAIPKICGEDLEGAVKLPASGVKTRCPPCNPGFFKTDNSTCEPCPYGSYSNGSDCTHCPAGTEPAVGFEYKWWNTLPSNMETTVLSGINFEYKGLTGWEVAGDHIYTAVGASDNDFMILTLVVPGFRPPQSVVADTENKEVARITFVFETICSVNCELYFMVGMNSRTNTPVETWKGTKGKQSYTYTIEENATVSFTWAFQRTTLHETGRKYTNDVAKIYSINVTNVMGGVASYCRPCALEASDLGSSCTSCPAGHYINRDSGTCHLCPSNTILKAHQPYGAQACVPCGPGTKNNKIHSLCYNDCTFSRNTPSRIFNYNFSALAGTVSLAGVPSFTSKGLKYFHHFTLSLCGNQGKKMAVCTDNVTDLRIPDGEAGFSKSVTAYVCQVVIIPSEVMGYKAGVSSQPVSLADRLVGVSTDMTLEGIVSPVELFHPETSGIPDIVFFFRSNDVTQSCSSGRSTTIRLRCNPMKAAPGTLRLPSMCSDGTCDGCNFHFLWESVAACPLCSASDYHTFVSSCVAGIQKTTYMWREPKLCSGGISLPEQRVTICKTIDFWLKVGISAGTCTAILLTVLTCYFWKKNQKLEYKYSKLVMNATLKDCDLPAADSCAIMEGEDVEDDFIFTSKKSLFGKIKSFTSKRTPDGFDSVPLKTSSGGPDMDM

Source

organism	Mus musculus
common_name	mice
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 polymer

description	Endosome/lysosome-associated apoptosis and autophagy regulator 1
formula_weight	110543.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,D

MKTIIALSYIFCLVFADYKDDDDKGSHHHHHHSGMELHACKESEYHFEYTACDSTGSRWRVAVPHSPGLCTSLPDPVKGTECSFSCNAGEFLDMKDQSCKPCAEGRYSLGTGIRFDEWDELPHGFASLSANLEVDDSISESTENCTSSKWVPRGDYIASNTDECTATLMYAVNLKQSGTVNFEYYYPDSSIIFEFFVQNDQCQPSADDSRWMKTTEKGWEFHSVELNRGNNVLYWRTTAFSVWSKVSKPVLVRNIAITGVAYTSECFPCKPGTYAAKQGSPFCKLCPANYYSNKGETSCHPCDADKYSEKGSSTCKVRPACTDKDYFYTHTACDAQGETQLMYKWAIPKICGEDLEGAVKLPASGVKTRCPPCNPGFFKTDNSTCEPCPYGSYSNGSDCTHCPAGTEPAVGFEYKWWNTLPSNMETTVLSGINFEYKGLTGWEVAGDHIYTAVGASDNDFMILTLVVPGFRPPQSVVADTENKEVARITFVFETICSVNCELYFMVGMNSRTNTPVETWKGTKGKQSYTYTIEENATVSFTWAFQRTTLHETGRKYTNDVAKIYSINVTNVMGGVASYCRPCALEASDLGSSCTSCPAGHYINRDSGTCHLCPSNTILKAHQPYGAQACVPCGPGTKNNKIHSLCYNDCTFSRNTPSRIFNYNFSALAGTVSLAGVPSFTSKGLKYFHHFTLSLCGNQGKKMAVCTDNVTDLRIPDGEAGFSKSVTAYVCQVVIIPSEVMGYKAGVSSQPVSLADRLVGVSTDMTLEGIVSPVELFHPETSGIPDIVFFFRSNDVTQSCSSGRSTTIRLRCNPMKAAPGTLRLPSMCSDGTCDGCNFHFLWESVAACPLCSASDYHTFVSSCVAGIQKTTYMWREPKLCSGGISLPEQRVTICKTIDFWLKVGISAGTCTAILLTVLTCYFWKKNQKLEYKYSKLVMNATLKDCDLPAADSCAIMEGEDVEDDFIFTSKKSLFGKIKSFTSKRTPDGFDSVPLKTSSGGPDMDM

Source

organism	Mus musculus
common_name	mice
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 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	syn
entity_count	3

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	12

Entity 5 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	3

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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	3.50 Å
resolution_method	—
num_particles	291029

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

Cryo-EM structure of Elapor1WT in tetrameric form

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

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)