SAXSdb — 9uav

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1. Structure Basics

entry_id	9uav
deposition_date	2025-04-01
title	Cryo-EM structure of HRD1-SEL1L-XTP3B (state D2) complex
keywords	ERAD, ALLERGEN; ALLERGEN
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	47.77 Å
rg_electron	46.78 Å
i0	544097000.00
molecular_weight	181360.0 kDa
excluded_volume	222150 Å³
envelope_volume	380880 Å³
shell_volume	69657 Å³
envelope_diameter	167.4 Å
shell_rg	49.64 Å
envelope_rg	46.16 Å
shape_rg	46.89 Å
total_rg	46.57 Å
total_atoms	12829
n_residues	1875
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	161.9 Å
rg_real	47.75 Å
rg_real_error	1.58 Å
i0_real	5.4410e+08
i0_real_error	1.0340e+07
rg_reciprocal	47.78 Å
i0_reciprocal	544100000.0000
total_estimate	0.6634
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	58.9 Å
skewness	0.284
kurtosis	-0.380
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	39740000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 0.044; Positv: 1.000; Valcen: 1.000; Smooth: 0.832

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	E3 ubiquitin-protein ligase synoviolin
formula_weight	30931.0 kDa
ec_number	2.3.2.27
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12831

MFRTAVMMAASLALTGAVVAHAYYLKHQFYPTVVYLTKSSPSMAVLYIQAFVLVFLLGKVMGKVFFGQLRAAEMEHLLERSWYAVTETCLAFTVFRDDFSPRFVALFTLLLFLKCFHWLAEDRVDFMERSPNISWLFHCRIVSLMFLLGILDFLFVSHAYHSILTRGASVQLVFGFEYAILMTMVLTIFIKYVLHSVDLQSENPWDNKAVYMLYTELFTGFIKVLLYMAFMTIMIKVHTFPLFAIRPMYLAMRQFKKAVTDAIMSR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Protein sel-1 homolog 1
formula_weight	61371.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

AKRRQMQEAEMMYQTGMKILNGSNKKSQKREAYRYLQKAASMNHTKALERVSYALLFGDYLPQNIQAAREMFEKLTEEGSPKGQTALGFLYASGLGVNSSQAKALVYYTFGALGGNLIAHMVLGYRYWAGIGVLQSCESALTHYRLVANHVASDISLTGGSVVQRIRLPDEVENPGMNSGMLEEDLIQYYQFLAEKGDVQAQVGLGQLHLHGGRGVEQNHQRAFDYFNLAANAGNSHAMAFLGKMYSEGSDIVPQSNETALHYFKKAADMGNPVGQSGLGMAYLYGRGVQVNYDLALKYFQKAAEQGWVDGQLQLGSMYYNGIGVKRDYKQALKYFNLASQGGHILAFYNLAQMHASGTGVMRSCHTAVELFKNVCERGRWSERLMTAYNSYKDGDYNAAVIQYLLLAEQGYEVAQSNAAFILDQREASIVGENETYPRALLHWNRAASQGYTVARIKLGDYHFYGFGTDVDYETAFIHYRLASEQQHSAQAMFNLGYMHEKGLGIKQDIHLAKRFYDMAAEASPDAQVPVFLALCKLGVVYFLQYIRE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Endoplasmic reticulum lectin 1
formula_weight	28985.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

LSDDIPFRVNWPGTEFSLPTTGVLYKEDNYVIMTTAHKEKYKCILPLVTSGDEEEEKDYKGPNPRELLEPLFKQSSCSYRIESYWTYEVCHGKHIRQYHEEKETGQKINIHEYYLGNMLAKNLLFEKEREAEEKEKSNEIPTKNIEGQMTPYYPVGMGNGTPCSLKQNRPRSSTVMYICHPESKHEILSVAEVTTCEYEVVILTPLLCSHPKYRFRASPVNDIFCQSLPGSPFKPLTLRQLEQQEEILR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	ALA-ASN-ALA
formula_weight	274.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

ANA

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-4)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1235.1 kDa
src_method	syn
entity_count	2

Entity 6 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	3.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.70 Å
resolution_method	—
num_particles	1905

fit	/app/data/saxs_computation/ua/9uav/9uav.fit
pddf	/app/data/pr_computation/ua/9uav/9uav.pr.out
profile	/app/data/saxs_computation/ua/9uav/9uav.dat

Cryo-EM structure of HRD1-SEL1L-XTP3B (state D2) complex

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

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)