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9rlt

dimerised 13S-13S+Beta5 proteasome precursor complexes

Method: ELECTRON MICROSCOPY D_max: 198.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rlt
deposition_date	2025-06-17
title	dimerised 13S-13S+Beta5 proteasome precursor complexes
keywords	proteasome biogenesis, Ump1, Pba1-2, cryo-EM, HYDROLASE; HYDROLASE
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	59.96 Å
rg_electron	59.92 Å
i0	6246270000.00
molecular_weight	674670.0 kDa
excluded_volume	846950 Å³
envelope_volume	1218000 Å³
shell_volume	162880 Å³
envelope_diameter	209.7 Å
shell_rg	67.68 Å
envelope_rg	58.25 Å
shape_rg	59.90 Å
total_rg	60.10 Å
total_atoms	47532
n_residues	6098
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	198.1 Å
rg_real	59.82 Å
rg_real_error	1.71 Å
i0_real	6.2460e+09
i0_real_error	1.1680e+08
rg_reciprocal	60.07 Å
i0_reciprocal	6249000000.0000
total_estimate	0.8652
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	76.2 Å
skewness	0.325
kurtosis	-0.243
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	1188000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.798

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4. Crystallography & Experiment

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5. Entities & Polymer Info (14)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A,O
atom_count	47532

MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVAIAEQD

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	D,R

MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQEQQEQDKKKKSNH

Entity 3 polymer

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

Polymer

type	polypeptide(L)
strand_id	E,S

MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKEAAESPEEADVEMS

Entity 4 polymer

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

Polymer

type	polypeptide(L)
strand_id	F,T

MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Entity 5 polymer

description	Proteasome maturation factor UMP1
formula_weight	18603.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	3,6

DYKDDDDKHHHHHHMNIVPQDTFKSQVSTDQDKSVLSSAVPSLPDTLRQQEGGAVPLSTQLNDRHPLESTLKNWETTQRQRQMEQYRQIFGIAEPMKRTMEMEIVNRTDFNPLSTNGSIHRDILLNKECSIDWEDVYPGTGLQASTMVGDDVHSKIEKQLGI

Source

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

Entity 6 polymer

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

Polymer

type	polypeptide(L)
strand_id	B,P

MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL

Entity 7 polymer

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

Polymer

type	polypeptide(L)
strand_id	C,Q

MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTGITKKDEDEEADEDMK

Entity 8 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	G,U

MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Entity 9 polymer

description	Proteasome subunit beta type-2
formula_weight	28299.9 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,W

MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTAVLKESIVNICDIQEEQVDITA

Source

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

Entity 10 polymer

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

Polymer

type	polypeptide(L)
strand_id	J,X

MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEVVKRYLKMRQD

Entity 11 polymer

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

Polymer

type	polypeptide(L)
strand_id	K,Y

MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVIVKIVDKDGIRQVDDFQAQ

Entity 12 polymer

description	Proteasome subunit beta type-5
formula_weight	31670.5 kDa
ec_number	3.4.25.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Z

MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHTDDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Entity 13 polymer

description	Proteasome chaperone 1
formula_weight	30718.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	7,4

MLFKQWNDLPEPKHLLDLPEISKNLQSLEVCPVPKVEFPQDLDVPQYSTAVITTKIMNPLFPKNLLQLTSIGEIKTTLTVKSPSLPQSSGKHSWNYDENFPNEVDPDQKNDTADETVYGFSFPIYSFGKTLLFSMEENFISISPIFGNMISRSIISQLAQFSPDIIVIGTSDKIASMKVMTENECTLQPPEFITGFIGSVLTQLIVGPSKGLKFKCLVAPSEGPNGFEKLSLSDMGSLVDLCGQWLGFEPSRYSEECYRLWRCDSAAIGAQSGLYI

Entity 14 polymer

description	Proteasome assembly chaperone 2
formula_weight	30762.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	8,5

MSCLVLPLVSVGNIPQLSIDWLLNSQANEWEYLEALDSKYLVEFVGPLDRPEDGSDSLYKDADMKYSSALEVFYNKKRGLFAIQQRTPLVSVNYLNNFIVEIILPFLSKYNISEICIWDSLYAMEDENGVIVRPQEVYSLGEFYFDDEAELLSNLHLNDQESMVNNWLHFTPTSFQDKISVDQPIFKILFQILNASQRPKALRSIKYCSCLANEGDNSLDSQQFLQWIISQKVIKNAPPIVKFVRPISWQGAYGMADARDKFVDLYN

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6. Citations (1)

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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	triclinic

resolution	3.09 Å
resolution_method	—
num_particles	156855

fit	/app/data/saxs_computation/rl/9rlt/9rlt.fit
pddf	/app/data/pr_computation/rl/9rlt/9rlt.pr.out
profile	/app/data/saxs_computation/rl/9rlt/9rlt.dat

dimerised 13S-13S+Beta5 proteasome precursor complexes

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

EM 3D

5. Entities & Polymer Info (14)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 polymer

Polymer

Source

Entity 10 polymer

Polymer

Entity 11 polymer

Polymer

Entity 12 polymer

Polymer

Entity 13 polymer

Polymer

Entity 14 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)