SAXSdb — 9sv3

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1. Structure Basics

entry_id	9sv3
deposition_date	2025-09-30
last_revision	2025-12-03
title	Local refinement of EloB/EloC/VHL/CV2a/14-3-3zeta/ERa from pose 1
keywords	E3 ligase, von Hippel-Lindau, VHL, 14-3-3, estrogen receptor alpha, PROTAC, proteolysis targeting chimera, degrader, LIGASE; 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	43.02 Å
rg_electron	41.08 Å
i0	203582000.00
molecular_weight	91718.0 kDa
excluded_volume	101450 Å³
envelope_volume	174060 Å³
shell_volume	38743 Å³
envelope_diameter	143.9 Å
shell_rg	41.49 Å
envelope_rg	40.80 Å
shape_rg	38.00 Å
total_rg	47.63 Å
total_atoms	9870
n_residues	820
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	143.9 Å
rg_real	43.38 Å
rg_real_error	1.55 Å
i0_real	2.0360e+08
i0_real_error	3.9730e+06
rg_reciprocal	43.03 Å
i0_reciprocal	203500000.0000
total_estimate	0.7970
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.1 Å
skewness	0.372
kurtosis	-0.838
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	7051000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.642; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.631; Smooth: 0.801

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Elongin-C
formula_weight	10974.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	9884

MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Elongin-B
formula_weight	11748.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Estrogen receptor
formula_weight	45511.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

MGHHHHHHGGSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGKKNALALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPTSRGGASVEETDQSHLATAGSTSSHSLQKYYITGEAEGRRATV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	14-3-3 protein zeta/delta
formula_weight	28819.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,D

MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGENWSHPQFEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 polymer

description	von Hippel-Lindau disease tumor suppressor
formula_weight	18702.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 6 non-polymer

description	;~{N}'-[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]-~{N}-[(2~{S})-2-[(1~{E},3~{R},4~{S},8~{R},9~{R},10~{R},11~{S},14~{S})-14-(methoxymethyl)-3,10-dimethyl-8-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(2-methylbut-3-en-2-yloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,9-bis(oxidanyl)-6-tricyclo[9.3.0.0^{3,7}]tetradeca-1,6-dienyl]propyl]tridecanediamide ;
formula_weight	1234.6 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	4.30 Å
resolution_method	—
num_particles	140642

fit	/app/data/saxs_computation/sv/9sv3/9sv3.fit
pddf	/app/data/pr_computation/sv/9sv3/9sv3.pr.out
profile	/app/data/saxs_computation/sv/9sv3/9sv3.dat

Local refinement of EloB/EloC/VHL/CV2a/14-3-3zeta/ERa from pose 1

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)