SAXSdb — 9qhi

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1. Structure Basics

entry_id	9qhi
deposition_date	2025-03-15
title	Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 0)
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	37.47 Å
rg_electron	36.78 Å
i0	395325000.00
molecular_weight	162350.0 kDa
excluded_volume	203780 Å³
envelope_volume	274000 Å³
shell_volume	61105 Å³
envelope_diameter	122.8 Å
shell_rg	43.90 Å
envelope_rg	35.99 Å
shape_rg	36.77 Å
total_rg	37.29 Å
total_atoms	11419
n_residues	1430
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	122.1 Å
rg_real	37.35 Å
rg_real_error	1.01 Å
i0_real	3.9530e+08
i0_real_error	7.2750e+06
rg_reciprocal	37.43 Å
i0_reciprocal	395400000.0000
total_estimate	0.8867
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	43.6 Å
skewness	0.271
kurtosis	-0.368
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	71470000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.918

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
formula_weight	36834.7 kDa
ec_number	2.3.2.24
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11419

GPANQEKKLGEYSKKAAMKPKPLSVLKSLEEKYVAVMKKLQFDTFEMVSEDEDGKLGFKVNYHYMSQVKNANDANSAARARRLAQEAVTLSTSLPLSSSSSVFVRCDEERLDIMKVLITGPADTPYANGCFEFDVYFPQDYPSSPPLVNLETTGGHSVRFNPNLYNDGKVCLSILNTWHGRPEEKWNPQTSSFLQVLVSVQSLILVAEPYFNEPGYERSRGTPSGTQSSREYDGNIRQATVKWAMLEQIRNPSPCFKEVIHKHFYLKRVEIMAQCEEWIADIQQYSSDKRVGRTMSHHAAALKRHTAQLREELLKLPCPEGLDPD

Source

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

Entity 2 polymer

description	Ubiquitin-like modifier-activating enzyme 6
formula_weight	118250.8 kDa
ec_number	6.2.1.45
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GPMEGSEPVAAHQGEEASCSSWGTGSTNKNLPIMSTASVEIDDALYSRQRYVLGDTAMQKMAKSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKCQAWDLGTNFFLSEDDVVNKRNRAEAVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQCVVLTEMKLPLQKKINDFCRSQCPPIKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEIFISNITQANPGIVTCLENHPHKLETGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDTTELEPYLHGGIAVQVKTPKTVFFESLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQEKYSRKPNVGCQQDSEELLKLATSISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGGVASQEVLKAVTGKFSPLCQWLYLEAADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQKLQNLNIFLVGCGAIGCEMLKNFALLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHHIQKPKSYTAADATLKINSQIKIDAHLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRYVDSRCLANLRPLLDSGTMGTKGHTEVIVPHLTESYNSHRDPPEEEIPFSTLKSFPAAIEHTIQWARDKFESSFSHKPSLFNKFWQTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRRPRNWSQCVELARLKFEKYFNHKALQLLHCFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEPLHLSFLQNAAKLYATVYCIPFAEEDLSADALLNILSEVKIQEFKPSNKVVQTDETARKPDHVPISSEDERNAIFQLEKAILSNEATKSDLQMAVLSFEKDDDHNGHIDFITAASNLRAKMYSIEPADRFKTKRIAGKIIPAIATTTATVSGLVALEMIKVTGGYPFEAYKNCFLNLAIPIVVFTETTEVRKTKIRNGISFTIWDRWTVHGKEDFTLLDFINAVKEKYGIEPTMVVQGVKMLYVPVMPGHAKRLKLTMHKLVKPTTEKKYVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Polyubiquitin-B
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	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	1

Entity 5 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	4.27 Å
resolution_method	—
num_particles	13888

fit	/app/data/saxs_computation/qh/9qhi/9qhi.fit
pddf	/app/data/pr_computation/qh/9qhi/9qhi.pr.out
profile	/app/data/saxs_computation/qh/9qhi/9qhi.dat

Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 0)

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)