8U6Y: Preholo-Proteasome from Beta 3 D205 deletion

Preholo-Proteasome from Beta 3 D205 deletion. Determined by electron microscopy at 2.8 Å resolution. Released 17 Apr 2024.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 34
Atoms: 57,080
Mol. weight: 919.96 kDa
Released: 17 Apr 2024

Explore 8U6Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U6Y contains 310 α-helices and 436 β-strands across 34 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains a and J: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	5
β-strand	21-25	5	5
β-strand	43-45	3	6
β-strand	49-55	7	6
α-helix	57-78	22
α-helix	81-83	3
α-helix	84-97	14
β-strand	105-112	8	6
β-strand	119-123	5	6
β-strand	124	1	7
β-strand	130	1	7
β-strand	136-140	5	5
α-helix	143-153	11
α-helix	160-172	13
β-strand	185-190	6	5
β-strand	195-200	6	5

Chains A and R: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	18-20	3
α-helix	26-34	9
β-strand	42-46	5	1
β-strand	50-56	7	1
β-strand	64	1	2
β-strand	72-74	3	3
β-strand	79-84	6	3
α-helix	87-108	22
α-helix	111-113	3
α-helix	114-130	17
β-strand	131	1	4
β-strand	140-147	8	3
β-strand	151-157	7	3
β-strand	163-166	4	3
β-strand	169-171	3	1
α-helix	175-185	11
α-helix	199-214	16
β-strand	223-229	7	1
β-strand	233-235	3	1
α-helix	236-237	2
α-helix	238-249	12

Chains b and K: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	13
β-strand	13-17	5	13
β-strand	35-39	5	14
β-strand	42-48	7	14
α-helix	52-71	20
α-helix	74-76	3
α-helix	77-93	17
α-helix	96-99	4
β-strand	100-108	9	14
β-strand	113-119	7	14
β-strand	125-127	3	14
β-strand	130-132	3	13
α-helix	144-146	3
α-helix	154-171	18
β-strand	180-185	6	13
β-strand	188-191	4	13

Chains B and S: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	8
β-strand	18	1	8
α-helix	19-30	12
α-helix	32-33	2
β-strand	34-38	5	9
β-strand	43-48	6	9
β-strand	56	1	3
α-helix	58-60	3
β-strand	65-68	4	10
β-strand	71-77	7	10
α-helix	79-92	14
α-helix	93-98	6
α-helix	99-101	3
α-helix	104-106	3
α-helix	107-123	17
β-strand	127	1	4
α-helix	128-130	3
β-strand	132-140	9	10
β-strand	144-150	7	10
β-strand	156-158	3	10
β-strand	159	1	11
β-strand	161-164	4	9
α-helix	168-178	11
α-helix	185-199	15
β-strand	209-214	6	9
α-helix	219-221	3
β-strand	224-225	2	12
β-strand	235-237	3	9
α-helix	238-239	2
α-helix	240-247	8

Chains c and L: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	23-28	6
α-helix	35-38	4
β-strand	44-45	2	108
α-helix	52-57	6
β-strand	77-83	7	19
β-strand	86-89	4	19
β-strand	109-113	5	20
β-strand	116-119	4	20
β-strand	122	1	21
α-helix	124-145	22
α-helix	148-150	3
α-helix	151-164	14
β-strand	172	1	21
β-strand	175-180	6	20
β-strand	184-190	7	20
β-strand	196-197	2	20
β-strand	201-205	5	19
α-helix	208-216	9
α-helix	225-237	13
β-strand	253-256	4	19
β-strand	259-262	4	19

Chains C and T: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	20-29	10
α-helix	33-34	2
β-strand	35-40	6	15
β-strand	43-49	7	15
β-strand	57	1	11
β-strand	66-70	5	16
β-strand	73-79	7	16
α-helix	81-102	22
α-helix	105-107	3
α-helix	108-121	14
β-strand	125	1	17
α-helix	129-131	3
β-strand	133-141	9	16
β-strand	145-151	7	16
β-strand	157-159	3	16
β-strand	160	1	18
β-strand	162-165	4	15
α-helix	169-179	11
α-helix	186-200	15
α-helix	208-210	3
β-strand	211-217	7	15
β-strand	226-229	4	15
α-helix	230-231	2
α-helix	232-242	11

Chains d and M: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	25
β-strand	39-45	7	25
β-strand	48-50	3	26
β-strand	53-56	4	26
β-strand	63-66	4	27
β-strand	69-75	7	27
α-helix	77-97	21
α-helix	105-117	13
β-strand	126-133	8	27
β-strand	139-144	6	27
β-strand	150-153	4	27
β-strand	155-159	5	25
α-helix	162-172	11
α-helix	188-190	3
α-helix	196-213	18
β-strand	214	1	54
β-strand	220-227	8	25
β-strand	230-237	8	25

Chains D and U: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	18-28	11
α-helix	31-32	2
β-strand	33-37	5	22
β-strand	42-45	4	22
β-strand	55	1	18
β-strand	65-68	4	23
β-strand	71-77	7	23
α-helix	79-99	21
α-helix	103-105	3
α-helix	106-119	14
β-strand	126	1	17
α-helix	127-129	3
β-strand	131-137	7	23
β-strand	146-150	5	23
β-strand	156-158	3	23
β-strand	159	1	24
β-strand	161-164	4	22
α-helix	168-178	11
α-helix	188-200	13
β-strand	212-216	5	22
β-strand	220-223	4	22
α-helix	229-236	8

9 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proteasome subunit alpha type-1	A, R	protein	252	Saccharomyces cerevisiae S288C	P21243 (AlphaFold model)
Proteasome subunit alpha type-2	B, S	protein	250	Saccharomyces cerevisiae S288C	P23639 (AlphaFold model)
Proteasome subunit alpha type-3	C, T	protein	245	Saccharomyces cerevisiae S288C	P23638 (AlphaFold model)
Proteasome subunit alpha type-4	D, U	protein	254	Saccharomyces cerevisiae S288C	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	E, V	protein	260	Saccharomyces cerevisiae S288C	P32379
Proteasome subunit alpha type-6	F, W	protein	234	Saccharomyces cerevisiae S288C	P40302
Proteasome subunit alpha type-7	G, X	protein	288	Saccharomyces cerevisiae S288C	P21242
Proteasome maturation factor UMP1	H, Y	protein	148	Saccharomyces cerevisiae S288C	P38293
Proteasome subunit beta type-2	I, Z	protein	261	Saccharomyces cerevisiae S288C	P25043
Proteasome subunit beta type-3	J, a	protein	204	Saccharomyces cerevisiae S288C	P25451
Proteasome subunit beta type-4	K, b	protein	198	Saccharomyces cerevisiae S288C	P22141
Proteasome subunit beta type-5	L, c	protein	287	Saccharomyces cerevisiae S288C	P30656

5 more molecules are not listed.

Sequence of entity 1 (A, R), FASTA

>8U6Y_1 Proteasome subunit alpha type-1 (chains A, R)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 2 (B, S), FASTA

>8U6Y_2 Proteasome subunit alpha type-2 (chains B, S)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C, T), FASTA

>8U6Y_3 Proteasome subunit alpha type-3 (chains C, T)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGIT

Sequence of entity 4 (D, U), FASTA

>8U6Y_4 Proteasome subunit alpha type-4 (chains D, U)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 5 (E, V), FASTA

>8U6Y_5 Proteasome subunit alpha type-5 (chains E, V)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 6 (F, W), FASTA

>8U6Y_6 Proteasome subunit alpha type-6 (chains F, W)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G, X), FASTA

>8U6Y_7 Proteasome subunit alpha type-7 (chains G, X)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 8 (H, Y), FASTA

>8U6Y_8 Proteasome maturation factor UMP1 (chains H, Y)
MNIVPQDTFKSQVSTDQDKSVLSSAVPSLPDTLRQQEGGAVPLSTQLNDRHPLESTLKNW
ETTQRQRQMEQYRQIFGIAEPMKRTMEMEIVNRTDFNPLSTNGSIHRDILLNKECSIDWE
DVYPGTGLQASTMVGDDVHSKIEKQLGI

Sequence of entity 9 (I, Z), FASTA

>8U6Y_9 Proteasome subunit beta type-2 (chains I, Z)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 10 (J, a), FASTA

>8U6Y_10 Proteasome subunit beta type-3 (chains J, a)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQ

Sequence of entity 11 (K, b), FASTA

>8U6Y_11 Proteasome subunit beta type-4 (chains K, b)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 12 (L, c), FASTA

>8U6Y_12 Proteasome subunit beta type-5 (chains L, c)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Primary citation

Mechanism of autocatalytic activation during proteasome assembly. Velez, B., Walsh Jr., R.M., Rawson, S. et al. Nat Struct Mol Biol (2024) 31:1167-1175. DOI 10.1038/s41594-024-01262-1 · PubMed

Other PDB entries of the same protein (UniProt P21243 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RYP 1.9 Å, Crystal structure of the 20S proteasome from yeast at 2.4 Å resolution
8RVQ 2.02 Å, 20S proteasome from pre1-1
4R17 2.1 Å, Ligand-induced aziridine-formation at subunit beta5 of the yeast 20S proteasome
8RVL 2.14 Å, Proteasomal late precursor complex from pre1-1
8U7U 2.16 Å, Proteasome 20S Core Particle from Beta 3 D205 deletion
1G65 2.25 Å, Crystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity…
8RVP 2.28 Å, Proteasomal late precursor complex from pre1-1, state 2
4QVP 2.3 Å, yCP beta5-M45T mutant in complex with bortezomib
5CZ4 2.3 Å, Yeast 20S proteasome at 2.3 A resolution
6HWE 2.3 Å, Yeast 20S proteasome beta2-G45A mutant in complex with carfilzomib
9GBK 2.39 Å, Blm10-20S proteasome complex from pre1-1
1G0U 2.4 Å, A gated channel into the proteasome core particle

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