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9y0k

Structure of Plasmodium falciparum 20S proteasome with bound J80

Method: ELECTRON MICROSCOPY D_max: 189.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y0k
deposition_date	2025-08-28
title	Structure of Plasmodium falciparum 20S proteasome with bound J80
keywords	Proteasome, 20S proteasome, Plasmodium falciparum, proteasome inhibitor, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
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	60.03 Å
rg_electron	59.58 Å
i0	12736100000.00
molecular_weight	636200.0 kDa
excluded_volume	618100 Å³
envelope_volume	1242700 Å³
shell_volume	167350 Å³
envelope_diameter	193.4 Å
shell_rg	67.59 Å
envelope_rg	57.41 Å
shape_rg	59.58 Å
total_rg	59.70 Å
total_atoms	48226
n_residues	6248
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	189.0 Å
rg_real	59.73 Å
rg_real_error	1.74 Å
i0_real	1.2740e+10
i0_real_error	2.7330e+08
rg_reciprocal	60.26 Å
i0_reciprocal	12750000000.0000
total_estimate	0.8099
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	80.0 Å
skewness	0.192
kurtosis	-0.436
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	886000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (15)

Entity 1 polymer

description	Proteasome subunit alpha type-6
formula_weight	29531.7 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,O
atom_count	48226

MVRPSQSMYDRHLTIFSPDGNLYQIEYAIKAVKNTNITSVGVKGENCAVIISQKKMATQYISQDKLLDYNNITNIYNITDEIGCSMVGMPGDCLSMVYKARSEASEFLYSNGYNVNAETLCRNICDKIQVYTQHAYMRLHACSGMIIGIDENNKPELFKFDPSGFCAGYRACVIGNKEQESISVLERLLEKRKKKIQQETIDEDIRNTTILAIEALQTILAFDLKASEIEVAIVSTKNRNFTQISEKEIDNYLTYIAERD

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Proteasome subunit alpha type-2
formula_weight	26556.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,P

MADGEYSFSLTTFSPTGKLVQIEYALNRVSSSSPALGIRAKNGVIIATEKKSPNELIEENSIFKIQQISEHIGIVYAGMPGDFRVLLKRARKEAIRYSLQYGSEILVKELVKIIASIVQEFTQTGGVRPFGLSLLICGVDVYGYHLYQIDPSGCYFNWMATCVGKDYQNNMSFLEKRYNKDIEIEDAIHTAILTLKESYEGVLNEKNIEIGVAYDNKPFKILTQNEIKDYLIEIE

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Proteasome subunit alpha type-3
formula_weight	27977.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,Q

MARRYDSRTTTFSPEGRLYQVEYALEAINNASITIGLITKDGVILGADKVFISKLIDKANNYEKIYKIDKHIFCGVAGLNADANILINQSRLYAQRYLYNYNEVQPVSQLVVQICDIKQSYTQYGGLRPYGVSFLIGGYDTKDGYQLYHTDPSGNYSGWFATAIGTNNLTASSVLKQEWKNDMTLEEGLLLALKTLAKSTDTEIPKSEKIELAYLTNKDGEVYQKYLTEKEIEELIKLYTQKYIKE

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	Proteasome subunit alpha type-4
formula_weight	27263.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,R

MSYDRAITVFSPDGHLLQVEHALEAVKKGGCAVAIKSSNFAVLAVEKKNIPKLQNPKTTEKLIKLDEHNCLAFAGLNADARVLVNKTRLECQRYYLNMDEPAPVDYIAKYVAKVQQKFTHRGGVRPFGIATLIAGFKNNKEICIYQTEPSGIYAAWKAQAIGKNAKIVQEFLEKNYQENMEQKDCIFLALKAIFEVVELSSKNVEVALLTEKDLTFIEEQEINSMVELIDQERTKNNEQNE

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	Proteasome subunit alpha type-5
formula_weight	28417.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,S

MFSTRSEYDRGVNTFSPEGRLFQVEYALGAIKLGSTAVGICVNDGVILASERRISSTLIEKDSVEKLLSIDDHIGCAMSGLMADARTLIDYARVECNHYKFIYNENINIKSCVELISELALDFSNLSDSKRKKIMSRPFGVALLIGGVDKNGPCLWYTEPSGTNTRFSAASIGSAQEGAELLLQENYKKDMTFEQAEILALTVLRQVMEDKLSTSNVEICAIKKSDQTFYKYNTDDISRIIDVLPSPVYPTIDMTA

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 6 polymer

description	Proteasome subunit alpha type-1
formula_weight	28871.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,T

MYRNLYDTDNIIYSPEGRLYQVEYASEAIKQGTCAVAIKSKDYVVVSGLKKCISKLSFPQEKIFKIDDYIGISMSGITSDAKVLTKFMQNECLSHKFLYNENINIESLVRSVADKYQKNTQKSSKRAFGVGLMIAAYHNEPCIFETRPNGSYFEYDALSFGARSHASKTYLEKNLHLFEECSLEELILHCLKALKCSLSSESELTISNTALAVVGKNHPWQEISSLQLEEYLSKVKMDAEQEQVEENVQNEANE

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 7 polymer

description	Proteasome subunit alpha type-3
formula_weight	29324.3 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,U

MAGLSAGYDLSVSTFSPDGRLYQVEYIYKSINNNNTALCLECKDGIICCCINSNMDKNKMIKKNSYNRIYHVNNNIIITYSGFDGDARNIIDRARSEANTYYYNFHTNIPLHILVNRISLYIHAYTLYWHMRPFAASIIISSFNEKDKGDIYCIEPNGACYKYSGIVIGKNKEMFKTEIEKKDYKDINVRDAIEDIYKFILTSDDHMNKNNLQNLVNFSWICKESSYEFQNIHEEILTPALNKAVEYIEKLN

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 8 polymer

description	Proteasome endopeptidase complex
formula_weight	29143.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,V

TTIIGIIYDNGVMLACDSRTSSGTFISNKCSRKINRINENLYVCRSGASAHSQKIIEIIKHYCVSMKNENRKKGRFHEGETIYDETTYDEEIDIDSINYLDYNNNNDNNLVTKNKYFYEDKFNDYNPLVENVAHITKKIIYTNNNFLSCALIFGGYDKIKKQQLYAVNLNGSIIEKHDFAVSGSGSIYIQSYLQDKYKKFMTKKECFNLILNCVKYAMHNDNSSGGLIRIVNITKSFVEEFTVVNTQMNFQY

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 9 polymer

description	Proteasome subunit beta-2
formula_weight	25104.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,W

TTICGLVCQNAVILGADTRATEGPIVADKNCSKLHYISKNIWCAGAGVAGDLEHTTLWLQHNVELHRLNTNTQPRVSMCVSRLTQELFKYQGYKVCAIVLGGVDVNGPQLYGIHPHGSSCLLPFTALGSGSLNAMAVLEAKYRDNMTIEEGKNLVCEAICAGIFNDLGSGGNVDICVITKDSYQHIRPYKEPNMRLYHLPHPTIYPKGTTPILSEKIEYIKKFISVEDA

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 10 polymer

description	Proteasome subunit beta-3
formula_weight	24533.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	J,X

MGSIYNYNGGCVLGMSGSNCVAIACDLRLGANTFTTVSTKFSKIFKMNNNVYVGLSGLATDIQTLYEILRYRVNLYEVRQDAEMDVECFANMLSSILYSNRFSPYFVNPIVVGFKLKHYVDEEGEKKVNYEPYLTAYDLIGAKCETRDFVVNGVTSEQLFGMCESLYVKDQDENGLFETISQCLLSALDRDCISGWGAEVLVLTPEKIIKKKLKARMD

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 11 polymer

description	Proteasome subunit beta-4
formula_weight	22889.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,Y

MDTLIGLRGNNFVVLAADTYSINSIIKLKNDDNTKFYDIHGNKCLLLGGSIGDRLQFGEFIRKNVHLYQYQNNTDMFVKSFAFFTRKNLAYYLRRNPFEVNCLIAGYDKKDGYQLYWCDYLSNMDSVNKGAHGYGAYLVSAILDKYYHENLTVDEALDIFKLCFEELKKRFLLTQINYELRIMYDNKVETQYVTV

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 12 polymer

description	Proteasome subunit beta
formula_weight	23519.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,Z

TTLAFKFKDGIIVAVDSRASMGSFISSQNVEKIIEINKNILGTMAGGAADCLYWEKYLGKIIKIYELRNNEKISVRAASTILSNILYQYKGYGLCCGIILSGYDHTGFNMFYVDDSGKKVEGNLFSCGSGSTYAYSILDSAYDYNLNLDQAVELARNAIYHATFRDGGSGGKVRVFHIHKNGYDKIIEGEDVFDLHYHYTNPEQKDQYVM

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 13 polymer

description	Proteasome subunit beta
formula_weight	27301.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	M,a

MDLILYNDNLTEKKTEKENVIEHGRGFKRWYPYIDNGGTVIGLTGKDYVILAADTRLSLSYSIYTRFCPKISKLTDKCIIGSSGMQSDIKTLHSLLQKKIQLFVLEHSHYPDIHVIARLLCVILYSRRFFPYYAFNILAGVDENNKGVLYNYDSVGSYCEATHSCVGSGSQLILPILDNRVEQKNQLIKNTNFNLGDDINFVKDAITSATERDIYTGDKTLIYVIDKMGINVNTLDLKQD

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 14 polymer

description	Proteasome subunit beta
formula_weight	34823.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	N,b

MTLGPVVTGTSVIAIKYKHGIMIAADRKASYGSYAKFQNVERIFKINNKTVMGFSGELADAQYLHELLTRKNINNLSEKKRKEDMYTPQHYHSYVSRVFYVRKNRIDPLFNNIIIAGINSQKYDNNDDNVLLYTNKNNDDEQNEYKNNEEYKEIHKDDLYIGFVDMHGTNFCDDYITTGYARYFALTLLRDHYKDNMTEEEARILINECLRILYFRDATSSNFIQIVKVTSKGVEYEEPYILPCVLNSADYVYPSTLLPPAGCMWENLYFQSSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Plasmodium falciparum Dd2
ncbi_taxonomy_id	57267
host_organism	Spodoptera frugiperda

Entity 15 non-polymer

description	;N,N-diethyl-N~2~-hexanoyl-D-asparaginyl-N-{(1S)-2-(2,4-difluorophenyl)-1-[(2S,3S,5S,6S)-5-formyl-2-hydroxy-3-(hydroxymethyl)-3,6-dimethylmorpholin-2-yl]ethyl}-4-fluoro-L-phenylalaninamide ;
formula_weight	777.9 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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resolution	3.00 Å
resolution_method	—
num_particles	133662

fit	/app/data/saxs_computation/y0/9y0k/9y0k.fit
pddf	/app/data/pr_computation/y0/9y0k/9y0k.pr.out
profile	/app/data/saxs_computation/y0/9y0k/9y0k.dat

Structure of Plasmodium falciparum 20S proteasome with bound J80

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 (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)