8RVQ: 20S proteasome from pre1-1

20S proteasome from pre1-1. Determined by electron microscopy at 2.02 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 2.02 Å
Organism: Saccharomyces cerevisiae
Chains: 28
Atoms: 51,191
Mol. weight: 732.31 kDa
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8RVQ contains 241 α-helices and 392 β-strands across 28 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 1: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	1
β-strand	21-26	6	1
β-strand	29-30	2	2
β-strand	34	1	3
β-strand	35-37	3	2
β-strand	44-45	2	4
β-strand	51-56	6	4
α-helix	58-78	21
α-helix	86-98	13
β-strand	107-114	8	4
β-strand	120-125	6	4
β-strand	131-133	3	4
β-strand	136-140	5	1
α-helix	143-153	11
β-strand	160	1	5
β-strand	169	1	5
α-helix	170-172	3
α-helix	177-194	18
β-strand	195	1	6
β-strand	201-208	8	1
β-strand	211-218	8	1

Chain 2: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	10
β-strand	11-15	5	11
β-strand	19-25	7	11
β-strand	27-30	4	10
β-strand	33-37	5	10
β-strand	42-44	3	10
β-strand	49-56	8	10
α-helix	57-75	19
α-helix	89-105	17
β-strand	112-119	8	10
β-strand	125-131	7	10
β-strand	136-138	3	10
β-strand	141-143	3	11
α-helix	146-158	13
α-helix	162-164	3
α-helix	170-187	18
β-strand	188	1	12
β-strand	194-201	8	11
β-strand	207-213	7	11
α-helix	220-224	5

Chains A and O: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	26-34	9
β-strand	42-46	5	79
β-strand	51-55	5	79
β-strand	64	1	27
α-helix	66-68	3
β-strand	72-74	3	80
β-strand	80-84	5	80
α-helix	87-108	22
α-helix	111-113	3
α-helix	114-130	17
β-strand	131	1	81
α-helix	135-137	3
β-strand	140-147	8	80
β-strand	151-157	7	80
β-strand	163-166	4	80
β-strand	168-171	4	79
α-helix	175-188	14
α-helix	200-214	15
β-strand	224-229	6	79
β-strand	232-235	4	79
α-helix	238-244	7

Chains B and P: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	82
β-strand	12	1	83
β-strand	18	1	83
α-helix	19-29	11
α-helix	32-33	2
β-strand	34-38	5	84
β-strand	43-48	6	84
β-strand	56	1	80
α-helix	58-60	3
β-strand	65-68	4	85
β-strand	71-77	7	85
α-helix	79-93	15
α-helix	94-98	5
α-helix	99-101	3
α-helix	104-106	3
α-helix	107-120	14
β-strand	125	1	82
β-strand	127	1	81
α-helix	128-130	3
β-strand	132-140	9	85
β-strand	144-150	7	85
β-strand	156-158	3	85
β-strand	161-164	4	84
α-helix	168-177	10
α-helix	185-199	15
β-strand	209-214	6	84
α-helix	219-221	3
β-strand	224-225	2	31
β-strand	235-237	3	84
α-helix	238-239	2
α-helix	240-246	7

Chains C and Q: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	86
β-strand	19	1	86
α-helix	20-29	10
β-strand	35-40	6	87
β-strand	43-49	7	87
β-strand	66-68	3	88
β-strand	73-79	7	88
α-helix	81-102	22
α-helix	105-107	3
α-helix	108-124	17
β-strand	125	1	18
α-helix	129-131	3
β-strand	133-141	9	88
β-strand	145-151	7	88
β-strand	157-159	3	88
β-strand	160	1	16
β-strand	162-165	4	87
α-helix	169-177	9
α-helix	186-200	15
α-helix	208-210	3
β-strand	211-217	7	87
β-strand	226-229	4	87
α-helix	232-242	11

Chain D: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	18-29	12
α-helix	31-32	2
β-strand	33-37	5	15
β-strand	42-47	6	15
β-strand	55	1	16
β-strand	64-68	5	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	18
β-strand	131-138	8	17
β-strand	145-150	6	17
β-strand	156-157	2	17
β-strand	161-164	4	15
α-helix	168-178	11
α-helix	188-199	12
β-strand	210-216	7	15
β-strand	220-223	4	15
α-helix	224-225	2
α-helix	226-241	16

Chains E and S: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	89
α-helix	16	1
β-strand	21	1	89
α-helix	22-31	10
α-helix	35-36	2
β-strand	37-41	5	90
β-strand	46-51	6	90
α-helix	61-63	3
β-strand	67-71	5	91
β-strand	74-80	7	91
α-helix	82-84	3
α-helix	85-103	19
α-helix	106-108	3
α-helix	109-120	12
α-helix	121-123	3
β-strand	140-148	9	91
β-strand	152-158	7	91
β-strand	164-166	3	91
β-strand	167	1	21
β-strand	169-172	4	90
α-helix	176-186	11
α-helix	193-207	15
α-helix	211-212	2
β-strand	217-223	7	90
β-strand	227-230	4	90
α-helix	233-247	15

Chain F: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	20-30	11
α-helix	33-34	2
β-strand	35-39	5	19
β-strand	43-49	7	19
β-strand	52	1	20
β-strand	57	1	21
α-helix	58	1
β-strand	59	1	20
α-helix	60-61	2
β-strand	63-67	5	22
β-strand	70-76	7	22
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-117	13
α-helix	118-120	3
β-strand	122	1	23
α-helix	126-128	3
β-strand	130-138	9	22
β-strand	141-147	7	22
β-strand	153-155	3	22
β-strand	156	1	24
β-strand	158-161	4	19
α-helix	165-174	10
α-helix	176-180	5
α-helix	186-198	13
β-strand	211-217	7	19
β-strand	223-226	4	19
α-helix	227-233	7

14 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 beta type-6	1, M	protein	222	Saccharomyces cerevisiae	P23724 (AlphaFold model)
Proteasome subunit beta type-7	2, N	protein	233	Saccharomyces cerevisiae	P30657 (AlphaFold model)
Proteasome subunit alpha type-4	D, R	protein	254	Saccharomyces cerevisiae	P40303 (AlphaFold model)
Proteasome subunit alpha type-6	F, T	protein	234	Saccharomyces cerevisiae	P40302 (AlphaFold model)
Probable proteasome subunit alpha type-7	G, U	protein	288	Saccharomyces cerevisiae	P21242
Proteasome subunit beta type-1	H, V	protein	196	Saccharomyces cerevisiae	P38624
Proteasome subunit beta type-2	I, W	protein	232	Saccharomyces cerevisiae	P25043
Proteasome subunit beta type-3	J, X	protein	205	Saccharomyces cerevisiae	P25451
Proteasome subunit beta type-5	L, Z	protein	212	Saccharomyces cerevisiae	P30656
Proteasome subunit alpha type-1	A, O	protein	252	Saccharomyces cerevisiae	P21243
Proteasome subunit alpha type-2	B, P	protein	250	Saccharomyces cerevisiae	P23639
Proteasome subunit alpha type-3	C, Q	protein	258	Saccharomyces cerevisiae	P23638

2 more molecules are not listed.

Sequence of entity 1 (1, M), FASTA

>8RVQ_1 Proteasome subunit beta type-6 (chains 1, M)
QFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAAD
GDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRFFPYYVHTIIAGLDEDGKG
AVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEV
IKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKRD

Sequence of entity 2 (2, N), FASTA

>8RVQ_2 Proteasome subunit beta type-7 (chains 2, N)
TQQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDM
QHIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQ
SNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNA
MRVLYYRDARSSRNFSLAIIDKNTGLTFKKNLQVENMKWDFAKDIKGYGTQKI

Sequence of entity 3 (D, R), FASTA

>8RVQ_3 Proteasome subunit alpha type-4 (chains D, R)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 4 (F, T), FASTA

>8RVQ_4 Proteasome subunit alpha type-6 (chains F, T)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 5 (G, U), FASTA

>8RVQ_5 Probable proteasome subunit alpha type-7 (chains G, U)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 6 (H, V), FASTA

>8RVQ_6 Proteasome subunit beta type-1 (chains H, V)
TSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQ
YHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVH
KLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTA
AGVERLIFYPDEYEQL

Sequence of entity 7 (I, W), FASTA

>8RVQ_7 Proteasome subunit beta type-2 (chains I, W)
TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIG
SNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTD
VGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEI
GKDAEYLRNYLTPNVREEKQKSYKFPRGTTAVLKESIVNICDIQEEQVDITA

Sequence of entity 8 (J, X), FASTA

>8RVQ_8 Proteasome subunit beta type-3 (chains J, X)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 9 (L, Z), FASTA

>8RVQ_9 Proteasome subunit beta type-5 (chains L, Z)
TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLG
SQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGT
RLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHV
TEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Sequence of entity 10 (A, O), FASTA

>8RVQ_10 Proteasome subunit alpha type-1 (chains A, O)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 11 (B, P), FASTA

>8RVQ_11 Proteasome subunit alpha type-2 (chains B, P)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 12 (C, Q), FASTA

>8RVQ_12 Proteasome subunit alpha type-3 (chains C, Q)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Primary citation

Structural roles of Ump1 and beta-subunit propeptides in proteasome biogenesis. Mark, E., Ramos, P.C., Kayser, F. et al. Life Sci Alliance (2024) 7. DOI 10.26508/lsa.202402865 · PubMed

Other PDB entries of the same protein (UniProt P23724 (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
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
3NZJ 2.4 Å, Crystal structure of yeast 20S proteasome in complex with ligand 2a

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