1RYP: 20S proteasome from yeast

Crystal structure of the 20S proteasome from yeast at 2.4 Å resolution. Determined by X-ray diffraction at 1.9 Å resolution. Released 15 Apr 1998.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Saccharomyces cerevisiae
Chains: 28
Atoms: 52,604
Mol. weight: 706.52 kDa
Ligands: MG
Released: 15 Apr 1998

Explore 1RYP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RYP contains 245 α-helices and 398 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: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
β-strand	12-17	6	6
β-strand	20-22	3	7
β-strand	25-28	4	7
β-strand	35-36	2	8
β-strand	42-47	6	8
α-helix	49-69	21
α-helix	77-89	13
β-strand	98-105	8	8
β-strand	111-116	6	8
β-strand	122-125	4	8
β-strand	127-131	5	6
α-helix	134-144	11
β-strand	151	1	9
β-strand	160	1	9
α-helix	161-162	2
α-helix	164-167	4
α-helix	168-185	18
β-strand	186	1	40
β-strand	192-199	8	6
β-strand	202-209	8	6

Chain 2: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	-3--1	3	16
β-strand	3-8	6	17
β-strand	11-17	7	17
β-strand	20-22	3	16
β-strand	25-28	4	16
β-strand	34-37	4	16
β-strand	41-48	8	16
α-helix	49-67	19
α-helix	79-80	2
α-helix	81-97	17
β-strand	104-111	8	16
β-strand	117-123	7	16
β-strand	128-129	2	16
β-strand	133-135	3	17
α-helix	138-147	10
α-helix	154-159	6
α-helix	162-179	18
β-strand	180	1	37
β-strand	186-193	8	17
β-strand	197-205	9	17
α-helix	212-216	5

Chain A: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	26-34	9
β-strand	42-46	5	1
β-strand	50-56	7	1
β-strand	64	1	2
α-helix	66-68	3
β-strand	72-74	3	3
β-strand	80-84	5	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	163-165	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	223-229	7	1
β-strand	232-235	4	1
α-helix	238-248	11

Chain B: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	10
β-strand	12	1	11
β-strand	18	1	11
α-helix	19-29	11
α-helix	32-33	2
β-strand	34-39	6	12
β-strand	42-48	7	12
β-strand	56	1	5
α-helix	58-60	3
β-strand	65-68	4	13
β-strand	71-77	7	13
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	10
β-strand	127	1	4
β-strand	132-140	9	13
β-strand	144-150	7	13
β-strand	156-158	3	13
β-strand	159	1	14
β-strand	161-164	4	12
α-helix	168-178	11
α-helix	185-199	15
β-strand	209-214	6	12
α-helix	219-221	3
β-strand	224-225	2	15
β-strand	235-237	3	12
α-helix	238-239	2
α-helix	240-247	8

Chain C: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	13	1	18
β-strand	19	1	18
α-helix	20-29	10
α-helix	33-34	2
β-strand	35-40	6	19
β-strand	43-49	7	19
α-helix	50	1
β-strand	57	1	14
β-strand	66-68	3	20
β-strand	73-79	7	20
α-helix	81-102	22
α-helix	105-107	3
α-helix	108-124	17
β-strand	125	1	21
β-strand	133-141	9	20
β-strand	145-151	7	20
β-strand	157-159	3	20
β-strand	160	1	22
β-strand	162-165	4	19
α-helix	169-179	11
α-helix	186-200	15
α-helix	208-210	3
β-strand	211-217	7	19
α-helix	225	1
β-strand	226-229	4	19
α-helix	232-242	11

Chain D: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	23
β-strand	16	1	23
α-helix	18-27	10
α-helix	31-32	2
β-strand	33-37	5	24
β-strand	42-47	6	24
β-strand	55	1	22
β-strand	64-68	5	25
β-strand	71-77	7	25
α-helix	79-100	22
α-helix	103-105	3
α-helix	106-119	14
β-strand	126	1	21
β-strand	131-137	7	25
β-strand	146-150	5	25
β-strand	156-158	3	25
β-strand	159	1	26
β-strand	161-164	4	24
α-helix	168-176	9
α-helix	188-203	16
β-strand	210-216	7	24
β-strand	220-223	4	24
α-helix	226-236	11
α-helix	238-241	4

Chain E: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	27
α-helix	16	1
β-strand	21	1	27
α-helix	22-31	10
α-helix	35-36	2
β-strand	37-41	5	28
β-strand	46-51	6	28
β-strand	59	1	26
α-helix	61-63	3
β-strand	67-71	5	29
β-strand	74-80	7	29
α-helix	82-84	3
α-helix	85-103	19
α-helix	106-108	3
α-helix	109-117	9
β-strand	124	1	30
β-strand	134	1	30
β-strand	140-148	9	29
β-strand	152-158	7	29
β-strand	164-166	3	29
β-strand	167	1	31
β-strand	169-172	4	28
α-helix	176-186	11
α-helix	193-207	15
α-helix	211-212	2
β-strand	217-223	7	28
β-strand	227-230	4	28
α-helix	231-232	2
α-helix	233-247	15

Chain F: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	20-30	11
α-helix	33-34	2
β-strand	35-39	5	32
β-strand	43-49	7	32
β-strand	57	1	31
β-strand	63-67	5	33
β-strand	70-76	7	33
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-121	17
β-strand	122	1	34
β-strand	130-138	9	33
β-strand	141-147	7	33
β-strand	153-156	4	33
β-strand	158-161	4	32
α-helix	165-179	15
α-helix	186-197	12
β-strand	211-217	7	32
β-strand	220-226	7	32
α-helix	227-233	7

19 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
20S proteasome	A, O	protein	243	Saccharomyces cerevisiae	P21243 (AlphaFold model)
20S proteasome	B, P	protein	250	Saccharomyces cerevisiae	P23639 (AlphaFold model)
20S proteasome	C, Q	protein	244	Saccharomyces cerevisiae	P23638 (AlphaFold model)
20S proteasome	D, R	protein	241	Saccharomyces cerevisiae	P40303 (AlphaFold model)
20S proteasome	E, S	protein	242	Saccharomyces cerevisiae	P32379
20S proteasome	F, T	protein	233	Saccharomyces cerevisiae	P40302
20S proteasome	G, U	protein	244	Saccharomyces cerevisiae	P21242
20S proteasome	H, V	protein	205	Saccharomyces cerevisiae	P38624
20S proteasome	I, W	protein	222	Saccharomyces cerevisiae	P25043
20S proteasome	J, X	protein	204	Saccharomyces cerevisiae	P25451
20S proteasome	K, Y	protein	198	Saccharomyces cerevisiae	P22141
20S proteasome	L, Z	protein	212	Saccharomyces cerevisiae	P30656

2 more molecules are not listed.

Sequence of entity 1 (A, O), FASTA

>1RYP_1 20S PROTEASOME (chains A, O)
AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTV
SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYT
QRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKS
KIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVAIA
EQD

Sequence of entity 2 (B, P), FASTA

>1RYP_2 20S PROTEASOME (chains B, P)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C, Q), FASTA

>1RYP_3 20S PROTEASOME (chains C, Q)
GSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDT
STEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQG
YTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYK
DDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVK
TGIT

Sequence of entity 4 (D, R), FASTA

>1RYP_4 20S PROTEASOME (chains D, R)
GYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPS
KVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQ
SGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRK
EPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQE
Q

Sequence of entity 5 (E, S), FASTA

>1RYP_5 20S PROTEASOME (chains E, S)
DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIV
EIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGAS
GEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWH
SSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKEA
AE

Sequence of entity 6 (F, T), FASTA

>1RYP_6 20S PROTEASOME (chains F, T)
FRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQK
KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQ
SYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIK
IDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G, U), FASTA

>1RYP_7 20S PROTEASOME (chains G, U)
GTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKN
VKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHT
LYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHP
EGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFAQ
KEIN

Sequence of entity 8 (H, V), FASTA

>1RYP_8 20S PROTEASOME (chains H, V)
LKKGEVSLGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAAD
TQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAGYDDKNKGEVY
TIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSSGG
VIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 9 (I, W), FASTA

>1RYP_9 20S PROTEASOME (chains I, W)
TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIG
SNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTD
VGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEI
GKDAEYLRNYLTPNVREEKQKSYKFPRGTTAVLKESIVNICD

Sequence of entity 10 (J, X), FASTA

>1RYP_10 20S PROTEASOME (chains J, X)
SDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVT
TLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFI
AGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALS
GWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 11 (K, Y), FASTA

>1RYP_11 20S PROTEASOME (chains K, Y)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 12 (L, Z), FASTA

>1RYP_12 20S PROTEASOME (chains L, Z)
TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLG
SQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGT
RLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHV
TEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	20

Primary citation

Structure of 20S proteasome from yeast at 2.4 A resolution. Groll, M., Ditzel, L., Lowe, J. et al. Nature (1997) 386:463-471. DOI 10.1038/386463a0 · PubMed

Other PDB entries of the same protein (UniProt P21243 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
3NZJ 2.4 Å, Crystal structure of yeast 20S proteasome in complex with ligand 2a

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1RYP is part of these collections:

Protein folding, misfolding and amyloid

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