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9qbo

Yeast 20S proteasome mutant: beta5_G128V (b5-propeptide in trans) in complex with MG132

Method: X-RAY DIFFRACTION D_max: 189.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qbo
deposition_date	2025-03-03
title	Yeast 20S proteasome mutant: beta5_G128V (b5-propeptide in trans) in complex with MG132
keywords	Proteasome, Proteasome Associated Autoinflammatory Syndromes, Mutation, Assembly, Maturation, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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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	60.14 Å
rg_electron	59.66 Å
i0	13811600000.00
molecular_weight	654960.0 kDa
excluded_volume	632200 Å³
envelope_volume	1267800 Å³
shell_volume	169700 Å³
envelope_diameter	194.6 Å
shell_rg	68.08 Å
envelope_rg	57.78 Å
shape_rg	59.65 Å
total_rg	59.78 Å
total_atoms	49642
n_residues	6350
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	189.4 Å
rg_real	59.86 Å
rg_real_error	1.69 Å
i0_real	1.3810e+10
i0_real_error	2.6830e+08
rg_reciprocal	60.36 Å
i0_reciprocal	13820000000.0000
total_estimate	0.8457
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	80.1 Å
skewness	0.209
kurtosis	-0.417
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	1001000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.490

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4. Crystallography & Experiment

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5. Entities & Polymer Info (21)

Entity 1 polymer

description	Proteasome subunit alpha type-2
formula_weight	27191.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,O
atom_count	49864

MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL

Entity 2 polymer

description	Proteasome subunit alpha type-3
formula_weight	28748.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,P

MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTGITKKDEDEEADEDMK

Entity 3 polymer

description	Proteasome subunit alpha type-4
formula_weight	28478.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,Q

MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQEQQEQDKKKKSNH

Entity 4 polymer

description	Proteasome subunit alpha type-5
formula_weight	28649.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,R

MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKEAAESPEEADVEMS

Entity 5 polymer

description	Proteasome subunit alpha type-6
formula_weight	25634.0 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,S

MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Entity 6 polymer

description	Probable proteasome subunit alpha type-7
formula_weight	31575.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,T

MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Entity 7 polymer

description	Proteasome subunit alpha type-1
formula_weight	28033.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,U

MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVAIAEQD

Entity 8 polymer

description	Proteasome subunit beta type-2
formula_weight	25013.4 kDa
ec_number	3.4.25.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,V

TIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTAVLKESIVNICDIQEEQVDITA

Entity 9 polymer

description	Proteasome subunit beta type-3
formula_weight	22627.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,W

MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEVVKRYLKMRQD

Entity 10 polymer

description	Proteasome subunit beta type-4
formula_weight	22545.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	J,X

MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVIVKIVDKDGIRQVDDFQAQ

Entity 11 polymer

description	Proteasome subunit beta type-5
formula_weight	23266.2 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,Y

TTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVVSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Saccharomyces cerevisiae

Entity 12 polymer

description	Proteasome subunit beta type-6
formula_weight	24883.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,Z

QFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKRD

Entity 13 polymer

description	Proteasome subunit beta type-7
formula_weight	27200.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	M,a

TQIANAGASPMVNTQQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTGLTFKKNLQVENMKWDFAKDIKGYGTQKI

Entity 14 polymer

description	Proteasome subunit beta type-1
formula_weight	21416.1 kDa
ec_number	3.4.25.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	N,b

SIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Entity 15 polymer

description	3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
formula_weight	594.7 kDa
src_method	syn
entity_count	6

Polymer

type	polypeptide(L)
strand_id	f,g,h,i,j,k

XLLX

Entity 16 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 17 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 18 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 19 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	2

Entity 20 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	2

Entity 21 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	214

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6. Citations (1)

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length_a	137.190 Å
length_b	298.960 Å
length_c	146.780 Å
angle_alpha	90.00 °
angle_beta	112.98 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.800 Å
resolution_low	15.000 Å
r_factor	0.1779
r_work	0.1742
r_free	0.2125

fit	/app/data/saxs_computation/qb/9qbo/9qbo.fit
pddf	/app/data/pr_computation/qb/9qbo/9qbo.pr.out
profile	/app/data/saxs_computation/qb/9qbo/9qbo.dat

Yeast 20S proteasome mutant: beta5_G128V (b5-propeptide in trans) in complex with MG132

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

Diffraction

5. Entities & Polymer Info (21)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 polymer

Polymer

Entity 10 polymer

Polymer

Entity 11 polymer

Polymer

Source

Entity 12 polymer

Polymer

Entity 13 polymer

Polymer

Entity 14 polymer

Polymer

Entity 15 polymer

Polymer

Entity 16 non-polymer

Entity 17 non-polymer

Entity 18 non-polymer

Entity 19 non-polymer

Entity 20 non-polymer

Entity 21 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)