SAXSdb — 9qgr

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1. Structure Basics

entry_id	9qgr
deposition_date	2025-03-14
title	Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 4)
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	36.19 Å
rg_electron	35.35 Å
i0	388530000.00
molecular_weight	160630.0 kDa
excluded_volume	201560 Å³
envelope_volume	258990 Å³
shell_volume	59377 Å³
envelope_diameter	120.0 Å
shell_rg	43.11 Å
envelope_rg	34.90 Å
shape_rg	35.34 Å
total_rg	35.88 Å
total_atoms	11311
n_residues	1422
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	116.8 Å
rg_real	36.06 Å
rg_real_error	0.90 Å
i0_real	3.8850e+08
i0_real_error	6.7890e+06
rg_reciprocal	36.15 Å
i0_reciprocal	388600000.0000
total_estimate	0.8848
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.1 Å
skewness	0.261
kurtosis	-0.337
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	60070000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.877

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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	11311

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	3.10 Å
resolution_method	—
num_particles	20475

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

Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 4)

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)