9RL3: 13S proteasome precursor complex

13S proteasome precursor complex. Determined by electron microscopy at 3.31 Å resolution. Released 18 Mar 2026.

Method: Electron microscopy
Resolution: 3.31 Å
Organism: Saccharomyces cerevisiae
Chains: 13
Atoms: 23,220
Mol. weight: 351.87 kDa
Released: 18 Mar 2026

Explore 9RL3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RL3 contains 119 α-helices and 173 β-strands across 13 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 3: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	-11--6	6
α-helix	53-56	4
α-helix	60-75	16
α-helix	79-93	15
α-helix	105-110	6
α-helix	119-122	4
α-helix	138-146	9

Chain 4: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	18-20	3
α-helix	30-32	3
β-strand	35-37	3	20
β-strand	49-54	6	20
α-helix	55-57	3
α-helix	63-66	4
β-strand	69-79	11	20
α-helix	96-99	4
β-strand	103	1	5
α-helix	106-109	4
β-strand	117-127	11	20
β-strand	130-135	6	20
α-helix	144-158	15
β-strand	164-171	8	20
β-strand	178-181	4	20
β-strand	184	1	20
β-strand	193-194	2	21
α-helix	196-206	11
β-strand	214-220	7	20
β-strand	222	1	22
β-strand	229	1	22
α-helix	232-246	15
α-helix	250-261	12
β-strand	275	1	18

Chain 5: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	23
α-helix	11-13	3
α-helix	14-23	10
β-strand	31-35	5	23
β-strand	41	1	24
β-strand	44-45	2	21
β-strand	51	1	25
α-helix	55-57	3
β-strand	70-75	6	23
β-strand	80-85	6	23
β-strand	89	1	24
α-helix	95-97	3
α-helix	98-103	6
α-helix	104-110	7
β-strand	114-121	8	23
β-strand	131	1	26
β-strand	138-140	3	23
β-strand	144	1	23
α-helix	146-148	3
β-strand	165	1	27
β-strand	176	1	26
β-strand	179	1	27
α-helix	184-193	10
β-strand	204-211	8	23
α-helix	220-230	11
α-helix	237-240	4
β-strand	246	1	25
α-helix	247-251	5
β-strand	266	1	28

Chain A: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	26-33	8
α-helix	34-36	3
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	87-107	21
α-helix	111-113	3
α-helix	114-130	17
β-strand	131	1	4
β-strand	140-147	8	3
β-strand	151-156	6	3
β-strand	164-166	3	3
β-strand	168-169	2	1
α-helix	175-189	15
α-helix	199-210	12
α-helix	211-215	5
β-strand	223-228	6	1
β-strand	233-235	3	1
α-helix	238-249	12

Chain B: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	29
β-strand	18	1	29
α-helix	19-29	11
β-strand	34-39	6	30
β-strand	42-48	7	30
β-strand	56	1	3
α-helix	58-60	3
β-strand	65-68	4	31
β-strand	71-73	3	31
α-helix	79-92	14
α-helix	93-98	6
α-helix	99-101	3
α-helix	104-106	3
α-helix	107-119	13
α-helix	120-123	4
β-strand	127	1	4
α-helix	128-130	3
β-strand	134	1	32
β-strand	137-139	3	31
β-strand	145-147	3	31
β-strand	149-150	2	32
β-strand	156-157	2	32
β-strand	161-164	4	30
α-helix	169-177	9
α-helix	185-199	15
β-strand	209-214	6	30
α-helix	219-221	3
β-strand	235-237	3	30
α-helix	238-239	2
α-helix	240-247	8

Chain C: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	20-29	10
β-strand	39	1	33
β-strand	43-49	7	33
β-strand	66-68	3	34
β-strand	73-76	4	34
α-helix	81-102	22
α-helix	105-107	3
α-helix	108-121	14
β-strand	125	1	9
α-helix	129-131	3
β-strand	135-141	7	34
β-strand	145-151	7	34
β-strand	157-159	3	34
α-helix	169-178	10
α-helix	186-199	14
β-strand	211-218	8	33
β-strand	225-227	3	33
α-helix	229-231	3
α-helix	232-242	11

Chain D: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	18-27	10
β-strand	30	1	5
β-strand	33-34	2	6
β-strand	44-47	4	6
α-helix	48-52	5
β-strand	65-66	2	7
β-strand	71-73	3	7
β-strand	75-77	3	8
α-helix	79-100	22
α-helix	103-105	3
α-helix	106-119	14
β-strand	126	1	9
β-strand	131-133	3	8
β-strand	136-138	3	7
β-strand	145-150	6	7
β-strand	156-159	4	7
β-strand	163-164	2	6
α-helix	168-178	11
α-helix	188-202	15
β-strand	210-213	4	6
β-strand	215-216	2	10
β-strand	220-221	2	10
α-helix	226-243	18
α-helix	244-248	5

Chain E: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	23-31	9
β-strand	37-40	4	11
β-strand	41	1	12
β-strand	46	1	12
β-strand	49-51	3	11
β-strand	59	1	7
β-strand	67-69	3	13
β-strand	74-77	4	13
β-strand	78-80	3	14
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-120	12
α-helix	121-123	3
α-helix	130-132	3
β-strand	140-142	3	14
β-strand	145-146	2	13
β-strand	154-155	2	13
β-strand	157-158	2	14
β-strand	164-165	2	14
β-strand	169-172	4	11
α-helix	176-186	11
α-helix	193-206	14
α-helix	211-212	2
β-strand	217-219	3	11
β-strand	220-221	2	15
β-strand	222	1	12
β-strand	229-230	2	15
α-helix	231-232	2
α-helix	233-250	18

5 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-4	D	protein	254	Saccharomyces cerevisiae	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	E	protein	260	Saccharomyces cerevisiae	P32379 (AlphaFold model)
Proteasome subunit alpha type-6	F	protein	234	Saccharomyces cerevisiae	P40302 (AlphaFold model)
Proteasome maturation factor UMP1	3	protein	162	Saccharomyces cerevisiae	P38293
Proteasome chaperone 1	4	protein	276	Saccharomyces cerevisiae	Q05778
Proteasome assembly chaperone 2	5	protein	267	Saccharomyces cerevisiae	P36040
Proteasome subunit alpha type-2	B	protein	250	Saccharomyces cerevisiae	P23639
Proteasome subunit alpha type-3	C	protein	258	Saccharomyces cerevisiae	P23638
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

1 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9RL3_1 Proteasome subunit alpha type-1 (chains A)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 2 (D), FASTA

>9RL3_2 Proteasome subunit alpha type-4 (chains D)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 3 (E), FASTA

>9RL3_3 Proteasome subunit alpha type-5 (chains E)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 4 (F), FASTA

>9RL3_4 Proteasome subunit alpha type-6 (chains F)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 5 (3), FASTA

>9RL3_5 Proteasome maturation factor UMP1 (chains 3)
DYKDDDDKHHHHHHMNIVPQDTFKSQVSTDQDKSVLSSAVPSLPDTLRQQEGGAVPLSTQ
LNDRHPLESTLKNWETTQRQRQMEQYRQIFGIAEPMKRTMEMEIVNRTDFNPLSTNGSIH
RDILLNKECSIDWEDVYPGTGLQASTMVGDDVHSKIEKQLGI

Sequence of entity 6 (4), FASTA

>9RL3_6 Proteasome chaperone 1 (chains 4)
MLFKQWNDLPEPKHLLDLPEISKNLQSLEVCPVPKVEFPQDLDVPQYSTAVITTKIMNPL
FPKNLLQLTSIGEIKTTLTVKSPSLPQSSGKHSWNYDENFPNEVDPDQKNDTADETVYGF
SFPIYSFGKTLLFSMEENFISISPIFGNMISRSIISQLAQFSPDIIVIGTSDKIASMKVM
TENECTLQPPEFITGFIGSVLTQLIVGPSKGLKFKCLVAPSEGPNGFEKLSLSDMGSLVD
LCGQWLGFEPSRYSEECYRLWRCDSAAIGAQSGLYI

Sequence of entity 7 (5), FASTA

>9RL3_7 Proteasome assembly chaperone 2 (chains 5)
MSCLVLPLVSVGNIPQLSIDWLLNSQANEWEYLEALDSKYLVEFVGPLDRPEDGSDSLYK
DADMKYSSALEVFYNKKRGLFAIQQRTPLVSVNYLNNFIVEIILPFLSKYNISEICIWDS
LYAMEDENGVIVRPQEVYSLGEFYFDDEAELLSNLHLNDQESMVNNWLHFTPTSFQDKIS
VDQPIFKILFQILNASQRPKALRSIKYCSCLANEGDNSLDSQQFLQWIISQKVIKNAPPI
VKFVRPISWQGAYGMADARDKFVDLYN

Sequence of entity 8 (B), FASTA

>9RL3_8 Proteasome subunit alpha type-2 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 9 (C), FASTA

>9RL3_9 Proteasome subunit alpha type-3 (chains C)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 10 (G), FASTA

>9RL3_10 Probable proteasome subunit alpha type-7 (chains G)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 11 (I), FASTA

>9RL3_11 Proteasome subunit beta type-2 (chains I)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 12 (J), FASTA

>9RL3_12 Proteasome subunit beta type-3 (chains J)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Primary citation

Structural transitions in the stepwise assembly of proteasome core particles. Mark, E., Ramos, P.C., Nunes, M.M. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-70525-w · 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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