9D0T: Proteasome subunit alpha type-1

Proteasome core particle assembly intermediate Blm10:13S purified from Saccharomyces cerevisiae. Determined by electron microscopy at 2.84 Å resolution. Released 4 Dec 2024.

Method: Electron microscopy
Resolution: 2.84 Å
Organism: Saccharomyces cerevisiae
Chains: 12
Atoms: 34,073
Mol. weight: 540.82 kDa
Released: 4 Dec 2024

Explore 9D0T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D0T contains 211 α-helices and 156 β-strands across 12 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	26-34	9
β-strand	42-46	5	1
β-strand	50-55	6	1
β-strand	56	1	2
β-strand	64	1	3
β-strand	72-74	3	4
β-strand	79-84	6	4
α-helix	87-108	22
α-helix	114-128	15
β-strand	131	1	5
β-strand	140-147	8	4
β-strand	151-157	7	4
β-strand	163-166	4	4
β-strand	170-171	2	1
α-helix	175-189	15
α-helix	199-214	16
β-strand	223	1	2
β-strand	226-229	4	1
β-strand	232-235	4	1
α-helix	238-251	14

Chain B: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	11-12	2
β-strand	13	1	6
β-strand	17	1	6
α-helix	20-29	10
α-helix	32-33	2
β-strand	34-39	6	7
β-strand	42-48	7	7
β-strand	56-57	2	4
β-strand	65-68	4	8
β-strand	71-77	7	8
α-helix	79-92	14
α-helix	93-98	6
α-helix	99-101	3
α-helix	109-122	14
β-strand	127	1	5
α-helix	128-130	3
β-strand	132-138	7	8
β-strand	146-150	5	8
β-strand	156-158	3	8
β-strand	159	1	9
β-strand	161-164	4	7
α-helix	168-178	11
α-helix	185-199	15
β-strand	209-214	6	7
β-strand	224-225	2	10
β-strand	235-237	3	7
α-helix	238-239	2
α-helix	240-249	10

Chain C: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	13-14	2	11
β-strand	18-19	2	11
α-helix	20-29	10
β-strand	35-40	6	12
β-strand	43-49	7	12
β-strand	57	1	9
β-strand	66-70	5	13
β-strand	73-79	7	13
α-helix	81-102	22
α-helix	105-107	3
α-helix	108-124	17
β-strand	125	1	14
α-helix	129-131	3
β-strand	133-141	9	13
β-strand	145-151	7	13
β-strand	157-160	4	13
β-strand	162-165	4	12
α-helix	169-179	11
α-helix	186-198	13
β-strand	211-216	6	12
β-strand	217	1	15
β-strand	226	1	15
β-strand	229	1	12
α-helix	232-242	11

Chain D: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	19-29	11
α-helix	31-32	2
β-strand	33-37	5	16
β-strand	42-47	6	16
α-helix	48-52	5
β-strand	55	1	13
β-strand	65-68	4	17
β-strand	71-77	7	17
α-helix	79-100	22
α-helix	103-105	3
α-helix	106-122	17
β-strand	126	1	14
α-helix	127-129	3
β-strand	131-137	7	17
β-strand	146-150	5	17
β-strand	156-158	3	17
β-strand	159	1	18
β-strand	161-164	4	16
α-helix	168-178	11
α-helix	188-200	13
β-strand	210-215	6	16
β-strand	222-223	2	16
α-helix	224-225	2
α-helix	226-245	20

Chain E: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	22-28	7
α-helix	29-32	4
α-helix	35-36	2
β-strand	37-40	4	19
β-strand	46-51	6	19
α-helix	52-56	5
β-strand	59	1	18
α-helix	61-63	3
β-strand	67-71	5	20
β-strand	74-78	5	20
α-helix	83-103	21
α-helix	106-108	3
α-helix	109-121	13
β-strand	142-148	7	20
β-strand	152-158	7	20
β-strand	164-167	4	20
β-strand	169-172	4	19
α-helix	176-186	11
α-helix	193-207	15
α-helix	211-212	2
β-strand	217-223	7	19
β-strand	227-230	4	19
α-helix	231-232	2
α-helix	233-248	16

Chain F: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	20-27	8
α-helix	29-31	3
α-helix	33-34	2
β-strand	35-39	5	21
β-strand	44-49	6	21
β-strand	57	1	20
α-helix	58-61	4
β-strand	63-67	5	22
β-strand	70-75	6	22
β-strand	77	1	23
α-helix	81-94	14
α-helix	95-99	5
α-helix	105-121	17
β-strand	122	1	24
β-strand	131-138	8	22
β-strand	141-148	8	22
β-strand	152-155	4	22
β-strand	156	1	25
β-strand	158-161	4	21
α-helix	165-174	10
α-helix	177-180	4
α-helix	186-198	13
β-strand	211-216	6	21
β-strand	223-225	3	21
α-helix	227-230	4

Chain G: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
α-helix	35-36	2
β-strand	37-41	5	26
β-strand	45	1	27
β-strand	46-53	8	26
β-strand	59	1	25
β-strand	67-68	2	28
β-strand	74-80	7	28
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-122	14
β-strand	129	1	24
α-helix	130-132	3
β-strand	134-142	9	28
β-strand	145-151	7	28
β-strand	157-159	3	28
β-strand	160	1	3
β-strand	162-165	4	26
α-helix	169-182	14
α-helix	189-204	16
β-strand	212-218	7	26
β-strand	220	1	27
β-strand	229-231	3	26
α-helix	233-247	15

Chain I: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	29
α-helix	12-15	4
α-helix	22-26	5
β-strand	27-28	2	30
β-strand	32-35	4	10
β-strand	40-45	6	10
β-strand	63-67	5	30
β-strand	70-77	8	30
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-118	14
β-strand	125-133	9	30
β-strand	136-143	8	30
β-strand	147-150	4	30
β-strand	155-156	2	10
α-helix	160-170	11
α-helix	177-189	13
β-strand	203-208	6	10
β-strand	213-216	4	10
β-strand	241-247	7	31

4 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 activator BLM10	O	protein	2143	Saccharomyces cerevisiae	P43583
Proteasome maturation factor UMP1,Myosin light chain kinase 2, skeletal/cardiac muscle	P	protein	200	Saccharomyces cerevisiae	A4IFM7, P38293

Sequence of entity 1 (A), FASTA

>9D0T_1 Proteasome subunit alpha type-1 (chains A)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 2 (B), FASTA

>9D0T_2 Proteasome subunit alpha type-2 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C), FASTA

>9D0T_3 Proteasome subunit alpha type-3 (chains C)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 4 (D), FASTA

>9D0T_4 Proteasome subunit alpha type-4 (chains D)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 5 (E), FASTA

>9D0T_5 Proteasome subunit alpha type-5 (chains E)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 6 (F), FASTA

>9D0T_6 Proteasome subunit alpha type-6 (chains F)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G), FASTA

>9D0T_7 Probable proteasome subunit alpha type-7 (chains G)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 8 (I), FASTA

>9D0T_8 Proteasome subunit beta type-2 (chains I)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 9 (J), FASTA

>9D0T_9 Proteasome subunit beta type-3 (chains J)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 10 (K), FASTA

>9D0T_10 Proteasome subunit beta type-4 (chains K)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 11 (O), FASTA

>9D0T_11 Proteasome activator BLM10 (chains O)
MTANNDDDIKSPIPITNKTLSQLKRFERSPGRPSSSQGEIKRKKSRLYAADGRPHSPLRA
RSATPTLQDQKLFNGMDSTSLLNERLQHYTLDYVSDRAQHMKNIYDPSSRWFSRSVRPEF
PIEEFLPYKTESHEDQAKYLCHVLVNLYIAISSLDIQGLISISSKDLADLKKEVDDLALK
TDLFRLSNNTAENDLLGNDIADYDDAEGLEDELDEYFDLAGPDFNATGKITAKSATIVNV
NHWTNELKNCLHFDFPVALRKSLATVYYYLSLVQGQKVYRQMHVDMFERLVSLDDDRTNF
TELLQKQGLLLDHQIMLNFLCEFLPYPDPDYARYELSSKEDLQLFRLLLKHAHNAKPFFD
KSKESLLVDTMNFLLSSLAPSTMMAVMPIVTSVVPYHYHIHSKIIDYFPFCYSIWSSVSA
NVAIDTHMYDFVGSISKDVHNKILSSEHEKDVVGVEFGEFGIFTDDQMTFMFNRLQGHLR
TDGQIHSYSRTVKPFVYAINGSKKDRFFEKLVSLAKAIETFIHPSNNGFWTKPNAKFVHA
FIKSYHGRVKYEEDICARGVTNGICLTSFCHEEIVEIFLNIISLGSQNKNPDIANYYISC
FAYLLELDPSNAYLIYDKILIDLYDTLADQFINSRHRIISSLKQFTRVIRFIVMDKLYRV
HITNVLSMLVSKLDMNDTNLTSNLINGIVSIAAFIPIQDLTGEDDYISFESDTLPLVQQH
FYHIKCGESSKTFRVDDELLNNAFKASTTVFQSMLKVYVEKIFQLVDVDLEDSLVTKINQ
TTMILQESMDDKIFNYFASLLQRNFWSNDSFKEKDPNYELVTIPLAALVRRNNGLSKELV
RTLLFHIKEQIKRGAGSVRSTSEIQQRDVKLVLYLTALNDVLRQCHESLLEYSDELITFM
KYLYDNVTNPPLDVITSIVIHSALATLCTTEITDCRLFPEDSKIPEKDRWGGLQFDPRRF
DKQHLSFQWHVPSSDEITLSISILESLSEYCINNVEELMKAPRHDSEYGDMIQKYVLVMT
HTLSGSSLLFDPDFNKYRTQSNLSYREKLILLKNIRENNCDPQELDIDIEQIRSGKDDED
YIESKDIEAGLNAGVSDVVQLRDEFPDELIVDEEVVSEMPSGVNTPIAGTHGTDNSAMSS
DLAFRDLDIYTCNYYFGNTTEEKLQNPQYLQVHRVRARIGHFFHKLYVFLSTNFENNTNM
FQILLHGLKVWFTDLGQETVFNEDPNAFIDVDFLENVQSLSHVNEPFTRTNFAIRANSLH
QSRVLLHSTNRKASKLENLLLVDIIQLATSLYPDIYKPAQGTLVHCMKQLVGSYGVVINK
IIPSLEKAIKDHDYMKIQVILNVLLIKKIHRKLMTDYKDIGRLIFLLIECCRVNELEIGM
YADKILTDIVIGIKIPSSVCVISDQAFLPLAPPDGTINLQVEAVKLAKKKKREYYLSLLV
DLQDKLLDKLDNEKDMGWKIRMFILRFVTQIQSNLESKPDKRAVFSIISQISTKHPEIIH
LVVKSLLSTCNKIISLSDYEYDITRAYKNEFNPSFVEILDTSTTSFPKTFTEEMNNFDNP
KYFIDLRAYVGWLCWGRLMYVMSPKALKLNLRENELEVLKTAGHLLTREFLRDVTMNLVQ
DNETRGVFSSGNVSFFSLVILLISSGFCELNMSDLFELCESYYNKDDKASMIMSVEIVAG
LVCGSKFMSVSDLDKRDTFIENFLAKCLDYELNHDAFEIWSTLAWWLPAVVDLRRSKTFF
CHFINADGMFDRESDAATHQTSKIYMLRSILMSMEFRAPDVGKLFDELVFDHPYDQVRQA
VAKLLTTLVQNQSNPSISDPTTLLEAERNDPDGLGLPLKSVPEKVDAYIKKQFEIIKNLE
DSVVGLNPQQFIKTDYFYRTSTIFYWIKEMARGPNKVLLVPYLVDYVLPFLIGLVKHKDV
CALASLDPVRLYAGLGYMPIRKNHVAAIVDYVCSSNVALSSNQTKLQLAFIQHFLSAELL
QLTEEEKNKILEFVVSNLYNEQFVEVRVRAASILSDIVHNWKEEQPLLSLIERFAKGLDV
NKYTSKERQKLSKTDIKIHGNVLGLGAIISAFPYVFPLPPWIPKQLSNLSSWARTSGMTG
QAAKNTISEFKKVRADTWKFDRASFNTEELEDLEGVLWRSYYA

Sequence of entity 12 (P), FASTA

>9D0T_12 Proteasome maturation factor UMP1,Myosin light chain kinase 2, skeletal/cardiac muscle (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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