9D4U: Proteasome subunit alpha type-1

Core particle assembly intermediate Capless 13S purified from Saccharomyces cerevisiae. Determined by electron microscopy at 3.55 Å resolution. Released 20 Aug 2025.

Method: Electron microscopy
Resolution: 3.55 Å
Organism: Saccharomyces cerevisiae
Chains: 11
Atoms: 17,620
Mol. weight: 294.54 kDa
Released: 20 Aug 2025

Explore 9D4U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D4U contains 93 α-helices and 121 β-strands across 11 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.

Chain A: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	26-34	9
β-strand	42-46	5	1
β-strand	51-55	5	1
β-strand	64	1	2
α-helix	66-68	3
β-strand	72-76	5	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
α-helix	135-137	3
β-strand	140-147	8	3
β-strand	151-157	7	3
β-strand	163-166	4	3
β-strand	168-171	4	1
α-helix	175-189	15
α-helix	199-214	16
α-helix	220-222	3
β-strand	224-229	6	1
β-strand	232-235	4	1
α-helix	240-251	12

Chain B: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	20-29	10
α-helix	32-33	2
β-strand	34-39	6	5
β-strand	42-48	7	5
β-strand	56	1	3
β-strand	65-68	4	6
β-strand	71-77	7	6
α-helix	79-92	14
α-helix	93-98	6
α-helix	99-101	3
α-helix	104-106	3
α-helix	107-121	15
β-strand	127	1	4
α-helix	128-130	3
β-strand	132-140	9	6
β-strand	144-150	7	6
β-strand	156-159	4	6
β-strand	161-164	4	5
α-helix	168-178	11
α-helix	185-196	12
β-strand	209-214	6	5
α-helix	219-221	3
β-strand	224-225	2	7
β-strand	235-237	3	5
α-helix	240-249	10

Chain C: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	20-29	10
β-strand	34-40	7	8
β-strand	43-49	7	8
β-strand	57	1	6
β-strand	66-70	5	9
β-strand	73-79	7	9
α-helix	81-102	22
α-helix	105-107	3
α-helix	108-123	16
α-helix	129-131	3
β-strand	133-141	9	9
β-strand	145-151	7	9
β-strand	157-159	3	9
β-strand	160	1	10
β-strand	162-166	5	8
α-helix	169-179	11
α-helix	186-199	14
α-helix	208-210	3
β-strand	211-216	6	8
β-strand	217	1	11
β-strand	226	1	11
α-helix	228	1
β-strand	229	1	8
α-helix	230-231	2
α-helix	232-239	8

Chain D: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	21-27	7
α-helix	31-32	2
β-strand	33-37	5	12
β-strand	42-47	6	12
β-strand	55	1	10
β-strand	65-68	4	13
β-strand	71-77	7	13
α-helix	79-100	22
α-helix	106-122	17
α-helix	127-129	3
β-strand	131-137	7	13
β-strand	146-150	5	13
β-strand	157-158	2	13
β-strand	161-164	4	12
α-helix	168-176	9
α-helix	188-202	15
β-strand	210-215	6	12
β-strand	221-223	3	12
α-helix	230-245	16

Chain E: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	22-28	7
α-helix	31-33	3
β-strand	38-41	4	14
β-strand	46-51	6	14
β-strand	67-71	5	15
β-strand	74-77	4	15
β-strand	78	1	16
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-117	9
α-helix	118-121	4
α-helix	135-137	3
β-strand	142	1	16
β-strand	145-148	4	15
β-strand	152-155	4	15
β-strand	158	1	16
β-strand	170-171	2	14
α-helix	176-183	8
α-helix	193-204	12
β-strand	217-223	7	14
β-strand	227-230	4	14
α-helix	231-232	2
α-helix	236-246	11

Chain F: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	20-27	8
α-helix	33-34	2
β-strand	35-39	5	17
β-strand	43-49	7	17
α-helix	58-61	4
β-strand	64-65	2	18
β-strand	70-74	5	18
α-helix	78-99	22
α-helix	106-121	16
β-strand	122	1	19
α-helix	126-127	2
β-strand	132-137	6	18
β-strand	142-148	7	18
β-strand	152-154	3	18
β-strand	158-161	4	17
α-helix	166-174	9
α-helix	187-200	14
β-strand	211-217	7	17
β-strand	220	1	17
β-strand	225	1	17
α-helix	228-232	5

Chain G: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	20
β-strand	21	1	20
α-helix	22-33	12
β-strand	37-42	6	21
β-strand	45-54	10	21
β-strand	68-69	2	22
β-strand	74-79	6	22
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-122	14
β-strand	129	1	19
α-helix	130-132	3
β-strand	135-142	8	22
β-strand	145-151	7	22
β-strand	157-159	3	22
β-strand	160	1	2
β-strand	162-164	3	21
α-helix	169-175	7
α-helix	180-182	3
α-helix	189-202	14
α-helix	203-206	4
β-strand	211-220	10	21
β-strand	229-231	3	21
α-helix	233-247	15

Chain I: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
α-helix	23-25	3
β-strand	27-28	2	23
β-strand	32-37	6	7
β-strand	40-45	6	7
β-strand	63-67	5	24
β-strand	70-75	6	24
β-strand	76-77	2	23
α-helix	78-99	22
α-helix	105-118	14
β-strand	126-132	7	24
β-strand	137-142	6	24
β-strand	148-150	3	24
β-strand	153-156	4	7
α-helix	160-170	11
α-helix	177-189	13
β-strand	203-208	6	7
β-strand	213-216	4	7
β-strand	244-246	3	25

3 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	protein	252	Saccharomyces cerevisiae	P21243 (AlphaFold model)
Proteasome subunit alpha type-2	B	protein	250	Saccharomyces cerevisiae	P23639 (AlphaFold model)
Proteasome subunit alpha type-3	C	protein	258	Saccharomyces cerevisiae	P23638 (AlphaFold model)
Proteasome subunit alpha type-4	D	protein	254	Saccharomyces cerevisiae	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	E	protein	260	Saccharomyces cerevisiae	P32379
Proteasome subunit alpha type-6	F	protein	234	Saccharomyces cerevisiae	P40302
Probable proteasome subunit alpha type-7	G	protein	288	Saccharomyces cerevisiae	P21242
Proteasome subunit beta type-2	I	protein	261	Saccharomyces cerevisiae	P25043
Proteasome subunit beta type-3	J	protein	205	Saccharomyces cerevisiae	P25451
Proteasome subunit beta type-4	K	protein	198	Saccharomyces cerevisiae	P22141
Proteasome maturation factor UMP1	P	protein	200	Saccharomyces cerevisiae	P38293

Sequence of entity 1 (A), FASTA

>9D4U_1 Proteasome subunit alpha type-1 (chains A)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 2 (B), FASTA

>9D4U_2 Proteasome subunit alpha type-2 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C), FASTA

>9D4U_3 Proteasome subunit alpha type-3 (chains C)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 4 (D), FASTA

>9D4U_4 Proteasome subunit alpha type-4 (chains D)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 5 (E), FASTA

>9D4U_5 Proteasome subunit alpha type-5 (chains E)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 6 (F), FASTA

>9D4U_6 Proteasome subunit alpha type-6 (chains F)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G), FASTA

>9D4U_7 Probable proteasome subunit alpha type-7 (chains G)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 8 (I), FASTA

>9D4U_8 Proteasome subunit beta type-2 (chains I)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 9 (J), FASTA

>9D4U_9 Proteasome subunit beta type-3 (chains J)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 10 (K), FASTA

>9D4U_10 Proteasome subunit beta type-4 (chains K)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 11 (P), FASTA

>9D4U_11 Proteasome maturation factor UMP1 (chains P)
MNIVPQDTFKSQVSTDQDKSVLSSAVPSLPDTLRQQEGGAVPLSTQLNDRHPLESTLKNW
ETTQRQRQMEQYRQIFGIAEPMKRTMEMEIVNRTDFNPLSTNGSIHRDILLNKECSIDWE
DVYPGTGLQASTMVGDDVHSKIEKQLGIGRRIPGLINPWKRRWKKNFIAVSAANRFKKIS
SSGALDYDIPTTASENLYFQ

Primary citation

Structure of Blm10:13S proteasome intermediate reveals parallel assembly pathways for the proteasome core particle. Kaur, M., Chen, X., Lee, S.Y. et al. bioRxiv (2024). DOI 10.1101/2024.11.04.621988 · 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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