← Back to search

9yuz

Structure of the human 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.

Method: ELECTRON MICROSCOPY D_max: 193.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9yuz
deposition_date	2025-10-23
title	Structure of the human 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.
keywords	Proteasome, 20S, Inhibitor, Covalent, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	59.55 Å
rg_electron	59.14 Å
i0	12066600000.00
molecular_weight	613020.0 kDa
excluded_volume	592430 Å³
envelope_volume	1190900 Å³
shell_volume	162510 Å³
envelope_diameter	195.0 Å
shell_rg	66.64 Å
envelope_rg	56.92 Å
shape_rg	59.17 Å
total_rg	59.19 Å
total_atoms	46426
n_residues	6246
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

▼

3. P(r) Analysis (GNOM)

dmax	193.5 Å
rg_real	59.28 Å
rg_real_error	1.53 Å
i0_real	1.2070e+10
i0_real_error	2.5430e+08
rg_reciprocal	59.75 Å
i0_reciprocal	12080000000.0000
total_estimate	0.6290
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	74.4 Å
skewness	0.215
kurtosis	-0.406
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	764900000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 0.955; Smooth: 0.783

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (15)

Entity 1 polymer

description	Proteasome subunit alpha type-2
formula_weight	25927.5 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,O
atom_count	46426

MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Proteasome subunit alpha type-4
formula_weight	29525.8 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,P

MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHEEEEAKAEREKKEKEQKEKDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Proteasome subunit alpha type-7
formula_weight	27929.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,Q

MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENEKKKQKKAS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	Proteasome subunit alpha type-5
formula_weight	26436.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,R

MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKDI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	Proteasome subunit alpha type-1
formula_weight	29595.6 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,S

MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERPQRKAQPAQPADEPAEKADEPMEH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 6 polymer

description	Proteasome subunit alpha type-3
formula_weight	28469.3 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,T

MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYAKESLKEEDESDDDNM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 7 polymer

description	Proteasome subunit alpha type-6
formula_weight	27432.5 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,U

MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 8 polymer

description	Proteasome subunit beta type-7
formula_weight	30000.4 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,V

MAAVSVYAPPVGGFSFDNCRRNAVLEADFAKRGYKLPKVRKTGTTIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQMLFRYQGYIGAALVLGGVDVTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISKNKLDFLRPYTVPNKKGTRLGRYRCEKGTTAVLTEKITPLEIEVLEETVQTMDTS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 9 polymer

description	Proteasome subunit beta type-3
formula_weight	22972.9 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,W

MSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDKITTRTLKARMD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 10 polymer

description	Proteasome subunit beta type-2
formula_weight	22864.3 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	J,X

MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLPTFSVRIIDKNGIHDLDNISFPKQGS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 11 polymer

description	Proteasome subunit beta type-5
formula_weight	28510.2 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,Y

MALASVLERPLPVNQRGFFGLGGRADLLDLGPGSLSDGLSLAAPGWGVPEEPGIEMLHGTTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHEKYSGSTP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 12 polymer

description	Proteasome subunit beta type-1
formula_weight	26522.4 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,Z

MLSSTAMYSAPGRDLGMEPHRAAGPLQLRFSPYVFNGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGIREETVSLRKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 13 polymer

description	Proteasome subunit beta type-4
formula_weight	29231.2 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	M,a

MEAFLGSRSGLWAGGPAPGQFYRIPSTPDSFMDPASALYRGPITRTQNPMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGHSYSPRAIHSWLTRAMYSRRSKMNPLWNTMVIGGYADGESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRDARSYNRFQIATVTEKGVEIEGPLSTETNWDIAHMISGFE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 14 polymer

description	Proteasome subunit beta type-6
formula_weight	25377.7 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	N,b

MAATLLAARGAGPAPAWGPEAFTPDWESREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKFAVATLPPA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 15 non-polymer

description	;methyl N-{[(2R)-1-({(5R,8S)-5-[(3-fluorophenyl)methyl]-2,7-dioxo-1,6-diazacyclododecan-8-yl}amino)-1-oxo-3-phenylpropan-2-yl]carbamoyl}-L-valinate ;
formula_weight	625.7 kDa
src_method	syn
entity_count	2

▶

6. Citations (1)

▶

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	2.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.60 Å
resolution_method	—
num_particles	50210

fit	/app/data/saxs_computation/yu/9yuz/9yuz.fit
pddf	/app/data/pr_computation/yu/9yuz/9yuz.pr.out
profile	/app/data/saxs_computation/yu/9yuz/9yuz.dat

Structure of the human 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.

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 (15)

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 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 polymer

Polymer

Source

Entity 10 polymer

Polymer

Source

Entity 11 polymer

Polymer

Source

Entity 12 polymer

Polymer

Source

Entity 13 polymer

Polymer

Source

Entity 14 polymer

Polymer

Source

Entity 15 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)