SAXSdb — 9qgg

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1. Structure Basics

entry_id	9qgg
deposition_date	2025-03-13
title	Consensus structure of dUBA1-UbDha-dBIRC6 trapped ternary complex
keywords	Ubiquitin, E1, E2, Ligase, SIGNALING PROTEIN; LIGASE
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	35.89 Å
rg_electron	35.08 Å
i0	351156000.00
molecular_weight	152360.0 kDa
excluded_volume	191070 Å³
envelope_volume	245750 Å³
shell_volume	57094 Å³
envelope_diameter	120.0 Å
shell_rg	42.63 Å
envelope_rg	34.69 Å
shape_rg	35.08 Å
total_rg	35.60 Å
total_atoms	10729
n_residues	1349
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	117.6 Å
rg_real	35.78 Å
rg_real_error	0.66 Å
i0_real	3.5120e+08
i0_real_error	5.2780e+06
rg_reciprocal	35.85 Å
i0_reciprocal	351200000.0000
total_estimate	0.8821
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	42.8 Å
skewness	0.282
kurtosis	-0.303
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	55000000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.888

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	BIR repeat containing ubiquitin-conjugating enzyme, isoform B
formula_weight	35565.3 kDa
ec_number	2.3.2.23
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10729

GPEPQSKSIEQRYLELMKKRQFDTFDMIVESDNNSFRFVVSHHFEKMVRLAGDRYHPSRVKRLAQEAVTLSTSLPLSFSSSVFVRCDTDRLDIMKVLITGPADTPYANGCFEFDVFFPPDYPNQPMLINLETTGRHSVRFNPNLYNDGKVCLSVLNTWHGRPEEKWNAQTSSFLQVLVSIQSLILVPEPYFNEPGFERSRGSPSGTNSSREYNSNIYQACVRWAMLEQIRSPSQCFKDVIHKHFWLKREEICAQIEGWIEELGKPQYTERASRTISFNSMVLRRHYRHLREELSKLKPPRGLEDL

Source

organism	Drosophila melanogaster
common_name	fruit fly
ncbi_taxonomy_id	7227
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	E1 ubiquitin-activating enzyme
formula_weight	112045.2 kDa
ec_number	6.2.1.45
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GPMAGNSAAAGGDIDESLYSRQLYVLGHDAMRRMANSDILLSGLGGLGLEIAKNVILGGVKSITLHDTATCGLHDLSSQFYLTEADIGKNRAEASCAQLAELNNYVRTVSHTGPLTEEFLRKFRVVVLTNSDGEEQQRIAKFAHENGIALIIAETRGLFAKVFCDFGESFTIYDQDGTQPISTMIASITHDAQGVVTCLDETRHGFNDGDYVTFSEVQGMQELNGCQPLKITVLGPYTFSIGDTSKFGEYKSGGVATQVKMPKTISFKPLAQATEEPEFLISDFAKLDSPATLHVAFNALSCYRKAHNGALPRPWNEEDANSFLEVVRASSNAEVDEKLVLQFAKICSGNTCPLDAAVGGIVAQEVLKACSGKFTPIYQWLYFDALECLPTEGVEEADAQPVGSRYDSQIAIFGKKFQEKLADSKWFIVGAGAIGCELLKNFGMLGLGTGNGQIFVTDMDLIEKSNLNRQFLFRPHDVQKPKSMTAADAIKRMNPEVNVTAYELRVGAETEKVFSEDFFGKLDGVANALDNVDARIYMDRKCIFNRIPLVETGTLGTLGNVQVIVPFATESYSSSQDPPEKSIPICTLKNFPNAIEHTLQWARDAFEGVFKQSAENAAQYIADPQFTERIAKLPGIQPLEILDSIKKALIDDKPKSFAHCVEWARLYWEDQYVNQIKQLLFNFPPDQITSSGQPFWSGPKRCPDPLVFDVNDPMHLDFIYAAANLRAEVYGIEQVRNRETIAELVQKVKVPEFKPRSGVKIETNEAAAAASANNFDDGELDQDRVDKIISELLKNADKSSKITPLEFEKDDDSNLHMDFIVACSNLRAANYKIPPADRHKSKLIAGKIIPAIATTTSVLSGLAVLEVIKLIVGHRDLVKFKNGFANLALPFMAFSEPLPAAKNTYYGKEWTLWDRFEVTGELSLQEFLNYFEENEKLKITMLSQGVSMLYSFFMPKAKCSERLPLPMSEVVRRVSKRRLEPHERSLVFEICCNDVDGEDVEVPYVRYTLP

Source

organism	Drosophila melanogaster
common_name	fruit fly
ncbi_taxonomy_id	7227
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Polyubiquitin-C
formula_weight	8590.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,E

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	2.58 Å
resolution_method	—
num_particles	333479

fit	/app/data/saxs_computation/qg/9qgg/9qgg.fit
pddf	/app/data/pr_computation/qg/9qgg/9qgg.pr.out
profile	/app/data/saxs_computation/qg/9qgg/9qgg.dat

Consensus structure of dUBA1-UbDha-dBIRC6 trapped ternary complex

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)