9D3I: Proteasome subunit alpha type-1

Proteasome core particle assembly intermediate 5-alpha/4-beta/Ump1 purified from Saccharomyces cerevisiae. Determined by electron microscopy at 3.11 Å resolution. Released 20 Aug 2025.

Method: Electron microscopy
Resolution: 3.11 Å
Organism: Saccharomyces cerevisiae
Chains: 10
Atoms: 15,673
Mol. weight: 263.83 kDa
Released: 20 Aug 2025

Explore 9D3I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D3I contains 81 α-helices and 109 β-strands across 10 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: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	26-35	10
β-strand	42-46	5	1
β-strand	51-56	6	1
β-strand	64	1	2
α-helix	66-68	3
β-strand	72-74	3	3
β-strand	79-84	6	3
α-helix	87-108	22
α-helix	114-128	15
β-strand	131	1	4
α-helix	135-137	3
β-strand	140-147	8	3
β-strand	151-157	7	3
β-strand	163-165	3	3
β-strand	166	1	5
β-strand	168-171	4	1
α-helix	175-189	15
α-helix	199-214	16
β-strand	223-228	6	1
β-strand	233-235	3	1
α-helix	236-237	2
α-helix	238-251	14

Chain B: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	20-29	10
α-helix	32-33	2
β-strand	34-38	5	6
β-strand	43-48	6	6
β-strand	56	1	5
β-strand	65-68	4	7
β-strand	71-74	4	7
β-strand	77	1	8
α-helix	79-92	14
α-helix	93-98	6
α-helix	99-101	3
α-helix	104-106	3
α-helix	107-120	14
β-strand	127	1	4
α-helix	128-130	3
β-strand	132	1	8
β-strand	135-140	6	7
β-strand	144-150	7	7
β-strand	156-158	3	7
β-strand	159	1	9
β-strand	161-164	4	6
α-helix	168-178	11
α-helix	185-199	15
β-strand	209-214	6	6
α-helix	219-221	3
β-strand	224-225	2	10
β-strand	235-237	3	6
α-helix	238-239	2
α-helix	240-249	10

Chain C: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	20-29	10
β-strand	34-39	6	11
β-strand	43-49	7	11
β-strand	57	1	9
β-strand	66-68	3	12
β-strand	73-79	7	12
α-helix	81-102	22
α-helix	105-107	3
α-helix	108-121	14
β-strand	125	1	13
α-helix	129-131	3
β-strand	133-141	9	12
β-strand	145-151	7	12
β-strand	157-159	3	12
β-strand	160	1	14
β-strand	162-166	5	11
α-helix	169-179	11
α-helix	186-200	15
β-strand	211-217	7	11
β-strand	226-229	4	11
α-helix	232-241	10

Chain D: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	17-29	13
α-helix	31-32	2
β-strand	33-37	5	15
β-strand	42-47	6	15
α-helix	49-52	4
β-strand	55	1	14
α-helix	57-59	3
β-strand	65-68	4	16
β-strand	71-77	7	16
α-helix	79-100	22
α-helix	103-105	3
α-helix	106-122	17
β-strand	126	1	13
α-helix	127-129	3
β-strand	131-138	8	16
β-strand	145-150	6	16
β-strand	156-158	3	16
β-strand	161-164	4	15
α-helix	168-178	11
β-strand	180	1	17
β-strand	183	1	17
α-helix	188-202	15
β-strand	210-216	7	15
β-strand	220-223	4	15
α-helix	224-225	2
α-helix	226-245	20

Chain G: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
α-helix	35-36	2
β-strand	37-41	5	18
β-strand	45-54	10	18
β-strand	67-70	4	19
β-strand	74-80	7	19
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-122	14
β-strand	134-141	8	19
β-strand	146-151	6	19
β-strand	157-159	3	19
β-strand	160	1	2
β-strand	162-165	4	18
α-helix	169-182	14
α-helix	189-202	14
β-strand	211-220	10	18
β-strand	229-230	2	18
α-helix	234-247	14

Chain H: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	20
β-strand	11-13	3	20
β-strand	34-38	5	21
β-strand	41-44	4	21
α-helix	49-70	22
α-helix	73-74	2
α-helix	75-86	12
β-strand	98-101	4	21
α-helix	107-108	2
β-strand	109-112	4	21
β-strand	120-122	3	21
β-strand	124-127	4	20
α-helix	137-141	5
α-helix	148-158	11
β-strand	174-179	6	20
β-strand	183-187	5	20

Chain I: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7
α-helix	21-23	3
β-strand	27	1	22
β-strand	32-37	6	10
β-strand	40-47	8	10
β-strand	63-67	5	23
β-strand	70-76	7	23
β-strand	77	1	22
α-helix	78-99	22
α-helix	105-118	14
β-strand	125-133	9	23
β-strand	136-142	7	23
β-strand	148-150	3	23
β-strand	153-156	4	10
α-helix	160-170	11
α-helix	177-190	14
β-strand	201-208	8	10
β-strand	213-216	4	10

Chain J: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	24
β-strand	20-26	7	24
β-strand	43-45	3	25
β-strand	49-55	7	25
α-helix	57-78	22
α-helix	81-83	3
α-helix	84-96	13
β-strand	105-112	8	25
β-strand	119-123	5	25
β-strand	131-133	3	25
β-strand	136-139	4	24
α-helix	143-153	11
α-helix	160-174	15
β-strand	185-191	7	24
β-strand	194-199	6	24

2 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)
Probable proteasome subunit alpha type-7	G	protein	288	Saccharomyces cerevisiae	P21242
Proteasome maturation factor UMP1	P	protein	200	Saccharomyces cerevisiae	P38293
Proteasome subunit beta type-1	H	protein	215	Saccharomyces cerevisiae	P38624
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

Sequence of entity 1 (A), FASTA

>9D3I_1 Proteasome subunit alpha type-1 (chains A)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 2 (B), FASTA

>9D3I_2 Proteasome subunit alpha type-2 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C), FASTA

>9D3I_3 Proteasome subunit alpha type-3 (chains C)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 4 (D), FASTA

>9D3I_4 Proteasome subunit alpha type-4 (chains D)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 5 (G), FASTA

>9D3I_5 Probable proteasome subunit alpha type-7 (chains G)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 6 (P), FASTA

>9D3I_6 Proteasome maturation factor UMP1 (chains P)
MNIVPQDTFKSQVSTDQDKSVLSSAVPSLPDTLRQQEGGAVPLSTQLNDRHPLESTLKNW
ETTQRQRQMEQYRQIFGIAEPMKRTMEMEIVNRTDFNPLSTNGSIHRDILLNKECSIDWE
DVYPGTGLQASTMVGDDVHSKIEKQLGIGRRIPGLINPWKRRWKKNFIAVSAANRFKKIS
SSGALDYDIPTTASENLYFQ

Sequence of entity 7 (H), FASTA

>9D3I_7 Proteasome subunit beta type-1 (chains H)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 8 (I), FASTA

>9D3I_8 Proteasome subunit beta type-2 (chains I)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 9 (J), FASTA

>9D3I_9 Proteasome subunit beta type-3 (chains J)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 10 (K), FASTA

>9D3I_10 Proteasome subunit beta type-4 (chains K)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

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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