3NZJ: Yeast 20S proteasome

Crystal structure of yeast 20S proteasome in complex with ligand 2a. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Feb 2011.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Saccharomyces cerevisiae
Chains: 30
Atoms: 51,006
Mol. weight: 768.67 kDa
Released: 16 Feb 2011

Explore 3NZJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NZJ contains 245 α-helices and 397 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	-3--1	3	9
β-strand	4-8	5	10
β-strand	11-17	7	10
β-strand	20-22	3	9
β-strand	25-28	4	9
β-strand	34-37	4	9
β-strand	41-48	8	9
α-helix	49-67	19
α-helix	74-75	2
α-helix	76-92	17
β-strand	97-104	8	9
β-strand	108-114	7	9
β-strand	119-120	2	9
β-strand	124-126	3	10
α-helix	128-138	11
α-helix	14D-14F	3
α-helix	148-165	18
β-strand	166	1	59
β-strand	172-179	8	10
β-strand	183-191	9	10
α-helix	198-202	5

Chains 2 and N: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	16
β-strand	11-16	6	16
β-strand	20-22	3	17
β-strand	25-28	4	17
β-strand	34-38	5	18
β-strand	41-47	7	18
α-helix	49-70	22
α-helix	74-75	2
α-helix	76-89	14
β-strand	97-105	9	18
β-strand	107-113	7	18
β-strand	120-122	3	18
β-strand	124-127	4	16
α-helix	129-134	6
α-helix	135-141	7
α-helix	148-165	18
β-strand	166	1	56
β-strand	173-179	7	16
β-strand	183-18B	7	16
α-helix	18D-18G	4

Chain A: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
β-strand	15	1	2
β-strand	21	1	2
α-helix	22-33	12
α-helix	35-36	2
β-strand	37-42	6	3
β-strand	45-51	7	3
β-strand	59	1	4
α-helix	61-63	3
β-strand	68-71	4	5
β-strand	74-80	7	5
α-helix	82-96	15
α-helix	97-101	5
α-helix	102-103	3
α-helix	106-108	3
α-helix	109-122	14
β-strand	127	1	1
β-strand	129	1	6
β-strand	134-142	9	5
β-strand	146-151	7	5
β-strand	157-159	3	5
β-strand	160	1	7
β-strand	162-165	4	3
α-helix	169-179	11
α-helix	186-200	15
β-strand	210-215	6	3
α-helix	21D-21F	3
β-strand	21I-21J	2	8
β-strand	221-223	3	3
α-helix	224-225	2
α-helix	226-233	8

Chains B and P: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	15	1	11
β-strand	21	1	11
α-helix	22-31	10
α-helix	35-36	2
β-strand	37-42	6	12
β-strand	45-51	7	12
α-helix	52	1
β-strand	59	1	7
β-strand	67-69	3	13
β-strand	74-80	7	13
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-125	17
β-strand	126	1	14
α-helix	130-132	3
β-strand	134-142	9	13
β-strand	145-151	7	13
β-strand	157-159	3	13
β-strand	160	1	15
β-strand	162-165	4	12
α-helix	169-179	11
α-helix	186-200	15
α-helix	207-209	3
β-strand	210-216	7	12
β-strand	220-223	4	12
α-helix	226-235	10

Chains C and Q: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
α-helix	35-36	2
β-strand	37-41	5	19
β-strand	46-51	6	19
β-strand	59	1	15
α-helix	64-65	2
β-strand	68-71	4	20
β-strand	74-80	7	20
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-122	14
β-strand	129	1	14
β-strand	134-140	7	20
β-strand	147-151	5	20
β-strand	157-159	3	20
β-strand	160	1	21
β-strand	162-165	4	19
α-helix	169-177	9
α-helix	186-201	16
α-helix	207-209	3
β-strand	210-216	7	19
β-strand	220-223	4	19
α-helix	224-225	2
α-helix	226-241	16

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

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	22
α-helix	16	1
β-strand	21	1	22
α-helix	22-31	10
α-helix	35-36	2
β-strand	37-42	6	23
β-strand	45-51	7	23
β-strand	59	1	21
α-helix	61-63	3
β-strand	67-71	5	24
β-strand	74-80	7	24
α-helix	82-85	4
α-helix	86-103	18
α-helix	106-108	3
α-helix	109-120	12
β-strand	12A	1	25
β-strand	128	1	25
β-strand	134-142	9	24
β-strand	145-151	7	24
β-strand	157-159	3	24
β-strand	160	1	26
β-strand	162-165	4	23
α-helix	169-179	11
α-helix	186-200	15
α-helix	206-207	2
β-strand	210-216	7	23
β-strand	220-223	4	23
α-helix	224-225	2
α-helix	226-241	15

Chains E and S: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	22-32	11
α-helix	35-36	2
β-strand	37-41	5	27
β-strand	45-51	7	27
β-strand	54	1	28
β-strand	59	1	26
β-strand	63	1	28
β-strand	67-71	5	29
β-strand	74-80	7	29
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-122	14
β-strand	126	1	30
β-strand	134-142	9	29
β-strand	145-151	7	29
β-strand	157-159	3	29
β-strand	160	1	31
β-strand	162-165	4	27
α-helix	169-18C	15
α-helix	186-197	12
β-strand	210-216	7	27
β-strand	219-225	7	27
α-helix	226-232	7

Chain F: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	22-32	11
β-strand	37-42	6	32
β-strand	45-54	10	32
β-strand	59	1	31
α-helix	60	1
β-strand	68-70	3	33
β-strand	74-80	7	33
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-122	14
β-strand	129	1	30
β-strand	134-142	9	33
β-strand	145-151	7	33
β-strand	157-159	3	33
β-strand	160	1	34
β-strand	162-165	4	32
α-helix	169-18B	14
α-helix	186-201	15
α-helix	202-205	4
β-strand	207-216	10	32
β-strand	222-223	2	32
α-helix	226-239	14

12 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 component Y7	A, O	protein	250	Saccharomyces cerevisiae	P23639 (AlphaFold model)
Proteasome component Y13	B, P	protein	258	Saccharomyces cerevisiae	P23638 (AlphaFold model)
Proteasome component PRE6	C, Q	protein	254	Saccharomyces cerevisiae	P40303 (AlphaFold model)
Proteasome component PUP2	D, R	protein	260	Saccharomyces cerevisiae	P32379 (AlphaFold model)
Proteasome component PRE5	E, S	protein	234	Saccharomyces cerevisiae	P40302
Proteasome component C1	F, T	protein	288	Saccharomyces cerevisiae	P21242
Proteasome component C7-alpha	G, U	protein	252	Saccharomyces cerevisiae	P21243
Proteasome component PUP1	H, V	protein	261	Saccharomyces cerevisiae	P25043
Proteasome component PUP3	I, W	protein	205	Saccharomyces cerevisiae	P25451
Proteasome component C11	J, X	protein	198	Saccharomyces cerevisiae	P22141
Proteasome component PRE2	K, Y	protein	287	Saccharomyces cerevisiae	P30656
Proteasome component C5	L, Z	protein	241	Saccharomyces cerevisiae	P23724

3 more molecules are not listed.

Sequence of entity 1 (A, O), FASTA

>3NZJ_1 Proteasome component Y7 (chains A, O)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 2 (B, P), FASTA

>3NZJ_2 Proteasome component Y13 (chains B, P)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 3 (C, Q), FASTA

>3NZJ_3 Proteasome component PRE6 (chains C, Q)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 4 (D, R), FASTA

>3NZJ_4 Proteasome component PUP2 (chains D, R)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 5 (E, S), FASTA

>3NZJ_5 Proteasome component PRE5 (chains E, S)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 6 (F, T), FASTA

>3NZJ_6 Proteasome component C1 (chains F, T)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 7 (G, U), FASTA

>3NZJ_7 Proteasome component C7-alpha (chains G, U)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 8 (H, V), FASTA

>3NZJ_8 Proteasome component PUP1 (chains H, V)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 9 (I, W), FASTA

>3NZJ_9 Proteasome component PUP3 (chains I, W)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 10 (J, X), FASTA

>3NZJ_10 Proteasome component C11 (chains J, X)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 11 (K, Y), FASTA

>3NZJ_11 Proteasome component PRE2 (chains K, Y)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Sequence of entity 12 (L, Z), FASTA

>3NZJ_12 Proteasome component C5 (chains L, Z)
MATIASEYSSEASNTPIEHQFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEP
KVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKR
FFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYE
PGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKR
D

Primary citation

20S proteasome inhibition: designing noncovalent linear peptide mimics of the natural product TMC-95A. Groll, M., Gallastegui, N., Marechal, X. et al. ChemMedChem (2010) 5:1701-1705. DOI 10.1002/cmdc.201000293 · 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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