4Y8L: Yeast 20S proteasome

Yeast 20S proteasome in complex with Ac-APLL-ep. Determined by X-ray diffraction at 2.4 Å resolution. Released 17 Jun 2015.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Saccharomyces cerevisiae S288c, synthetic construct
Chains: 32
Atoms: 50,603
Mol. weight: 733.75 kDa
Ligands: MG
Released: 17 Jun 2015

Explore 4Y8L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y8L contains 257 α-helices and 409 β-strands across 32 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
β-strand	6-8	3	9
β-strand	11-15	5	10
β-strand	19-25	7	10
β-strand	28-30	3	9
β-strand	33-36	4	9
β-strand	42-45	4	9
β-strand	49-56	8	9
α-helix	57-75	19
α-helix	87-88	2
α-helix	89-105	17
β-strand	112-119	8	9
β-strand	125-131	7	9
β-strand	136-138	3	9
β-strand	141-143	3	10
α-helix	146-156	11
α-helix	162-164	3
α-helix	170-187	18
β-strand	188	1	61
β-strand	194-201	8	10
β-strand	205-213	9	10
α-helix	220-224	5

Chain A: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	1
β-strand	12	1	2
β-strand	18	1	2
α-helix	19-30	12
α-helix	32-33	2
β-strand	34-38	5	3
β-strand	43-48	6	3
β-strand	56	1	4
β-strand	65-68	4	5
β-strand	71-77	7	5
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	1
β-strand	127	1	6
α-helix	128-130	3
β-strand	132-140	9	5
β-strand	144-150	7	5
β-strand	156-158	3	5
β-strand	159	1	7
β-strand	161-164	4	3
α-helix	168-178	11
α-helix	185-199	15
β-strand	209-214	6	3
α-helix	219-221	3
β-strand	224-225	2	8
β-strand	235-237	3	3
α-helix	238-239	2
α-helix	240-248	9

Chains b and N: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	15
β-strand	11-16	6	15
β-strand	20-22	3	16
β-strand	25-28	4	16
β-strand	34-38	5	17
β-strand	41-47	7	17
β-strand	48	1	16
α-helix	49-70	22
α-helix	73-74	2
α-helix	75-88	14
α-helix	90-92	3
β-strand	95-102	8	17
β-strand	108-113	6	17
β-strand	120-122	3	17
β-strand	124-127	4	15
α-helix	129-134	6
α-helix	135-141	7
α-helix	148-165	18
β-strand	166	1	58
β-strand	173-179	7	15
β-strand	183-188	6	15
α-helix	190-193	4

Chains B and P: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	12	1	11
β-strand	18	1	11
α-helix	19-28	10
α-helix	32-33	2
β-strand	34-39	6	12
β-strand	42-48	7	12
α-helix	49	1
β-strand	56	1	7
β-strand	65-67	3	13
β-strand	72-78	7	13
α-helix	80-101	22
α-helix	104-106	3
α-helix	107-123	17
β-strand	124	1	14
α-helix	127-130	4
β-strand	132-140	9	13
β-strand	144-150	7	13
β-strand	156-159	4	13
β-strand	161-164	4	12
α-helix	168-178	11
α-helix	185-199	15
α-helix	207-209	3
β-strand	210-216	7	12
β-strand	225-228	4	12
α-helix	231-240	10

Chains c, d, e and f: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	49

Chains C and Q: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	18
β-strand	15	1	18
α-helix	16-27	12
α-helix	29-30	2
β-strand	31-35	5	19
β-strand	40-45	6	19
β-strand	53	1	13
α-helix	59-60	2
β-strand	63-64	2	20
β-strand	69-75	7	20
α-helix	77-98	22
α-helix	101-103	3
α-helix	104-117	14
β-strand	124	1	14
α-helix	125-127	3
β-strand	129-135	7	20
β-strand	144-148	5	20
β-strand	154-156	3	20
β-strand	157	1	21
β-strand	159-162	4	19
α-helix	166-176	11
α-helix	186-198	13
β-strand	208-214	7	19
β-strand	218-221	4	19
α-helix	224-238	15

Chains D and R: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
β-strand	7	1	22
α-helix	8	1
β-strand	13	1	22
α-helix	14-24	11
α-helix	27-28	2
β-strand	29-33	5	23
β-strand	38-43	6	23
β-strand	51	1	21
α-helix	53-55	3
β-strand	59-63	5	24
β-strand	66-72	7	24
α-helix	74-76	3
α-helix	77-95	19
α-helix	98-100	3
α-helix	101-112	12
β-strand	115	1	25
β-strand	126	1	25
β-strand	132-140	9	24
β-strand	144-150	7	24
β-strand	156-158	3	24
β-strand	159	1	26
β-strand	161-164	4	23
α-helix	168-178	11
α-helix	185-199	15
α-helix	203-204	2
β-strand	209-215	7	23
β-strand	219-222	4	23
α-helix	223-224	2
α-helix	225-240	16

Chains E and S: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	19-30	12
α-helix	32-33	2
β-strand	34-38	5	27
β-strand	42-48	7	27
β-strand	51	1	28
β-strand	56	1	26
α-helix	57	1
β-strand	58	1	28
α-helix	59-60	2
β-strand	62-66	5	29
β-strand	69-75	7	29
α-helix	77-98	22
α-helix	101-103	3
α-helix	104-117	14
β-strand	121	1	30
β-strand	129-137	9	29
β-strand	140-146	7	29
β-strand	152-154	3	29
β-strand	155	1	31
β-strand	157-160	4	27
α-helix	164-178	15
α-helix	185-196	12
α-helix	197-199	3
β-strand	210-216	7	27
β-strand	219-224	6	27
α-helix	226-232	7

11 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-2	A, O	protein	250	Saccharomyces cerevisiae S288c	P23639 (AlphaFold model)
Proteasome subunit alpha type-3	B, P	protein	258	Saccharomyces cerevisiae S288c	P23638 (AlphaFold model)
Proteasome subunit alpha type-4	C, Q	protein	254	Saccharomyces cerevisiae S288c	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	D, R	protein	260	Saccharomyces cerevisiae S288c	P32379 (AlphaFold model)
Proteasome subunit alpha type-6	E, S	protein	234	Saccharomyces cerevisiae S288c	P40302
Probable proteasome subunit alpha type-7	F, T	protein	288	Saccharomyces cerevisiae S288c	P21242
Proteasome subunit alpha type-1	G, U	protein	252	Saccharomyces cerevisiae S288c	P21243
Proteasome subunit beta type-2	H, V	protein	232	Saccharomyces cerevisiae S288c	P25043
Proteasome subunit beta type-3	I, W	protein	205	Saccharomyces cerevisiae S288c	P25451
Proteasome subunit beta type-4	J, X	protein	198	Saccharomyces cerevisiae S288c	P22141
Proteasome subunit beta type-5	K, Y	protein	212	Saccharomyces cerevisiae S288c	P30656
Proteasome subunit beta type-6	L, Z	protein	222	Saccharomyces cerevisiae S288c	P23724

3 more molecules are not listed.

Sequence of entity 1 (A, O), FASTA

>4Y8L_1 Proteasome subunit alpha type-2 (chains A, O)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 2 (B, P), FASTA

>4Y8L_2 Proteasome subunit alpha type-3 (chains B, P)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 3 (C, Q), FASTA

>4Y8L_3 Proteasome subunit alpha type-4 (chains C, Q)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 4 (D, R), FASTA

>4Y8L_4 Proteasome subunit alpha type-5 (chains D, R)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 5 (E, S), FASTA

>4Y8L_5 Proteasome subunit alpha type-6 (chains E, S)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 6 (F, T), FASTA

>4Y8L_6 Probable proteasome subunit alpha type-7 (chains F, T)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 7 (G, U), FASTA

>4Y8L_7 Proteasome subunit alpha type-1 (chains G, U)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 8 (H, V), FASTA

>4Y8L_8 Proteasome subunit beta type-2 (chains H, V)
TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIG
SNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTD
VGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEI
GKDAEYLRNYLTPNVREEKQKSYKFPRGTTAVLKESIVNICDIQEEQVDITA

Sequence of entity 9 (I, W), FASTA

>4Y8L_9 Proteasome subunit beta type-3 (chains I, W)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 10 (J, X), FASTA

>4Y8L_10 Proteasome subunit beta type-4 (chains J, X)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 11 (K, Y), FASTA

>4Y8L_11 Proteasome subunit beta type-5 (chains K, Y)
TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLG
SQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGT
RLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHV
TEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Sequence of entity 12 (L, Z), FASTA

>4Y8L_12 Proteasome subunit beta type-6 (chains L, Z)
QFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAAD
GDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRFFPYYVHTIIAGLDEDGKG
AVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEV
IKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKRD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	7

Water and common crystallization additives (MES, CL) are not listed.

Primary citation

Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors. Huber, E.M., de Bruin, G., Heinemeyer, W. et al. J Am Chem Soc (2015) 137:7835-7842. DOI 10.1021/jacs.5b03688 · PubMed

Other PDB entries of the same protein (UniProt P23639 (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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