6J2N: Yeast proteasome in substrate-processing state

yeast proteasome in substrate-processing state (C3-b). Determined by electron microscopy at 7.5 Å resolution. Released 20 Mar 2019.

Method: Electron microscopy
Resolution: 7.5 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 47
Atoms: 106,100
Mol. weight: 1692.66 kDa
Released: 20 Mar 2019

Explore 6J2N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J2N contains 622 α-helices and 521 β-strands across 47 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	21-26	6	1
β-strand	31-36	6	1
β-strand	39-41	3	2
β-strand	44-47	4	2
β-strand	53-55	3	3
β-strand	61-66	6	3
α-helix	68-84	17
α-helix	85-89	5
α-helix	94-107	14
β-strand	114-121	8	3
β-strand	127-132	6	3
β-strand	139-141	3	3
β-strand	143-147	5	1
α-helix	156-159	4
α-helix	167-184	18
β-strand	185	1	4
β-strand	192-197	6	1
β-strand	202-207	6	1
α-helix	209-212	4

Chain 2: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	32-37	6	9
β-strand	40-46	7	9
β-strand	51	1	10
β-strand	54	1	10
β-strand	63-67	5	11
β-strand	70-76	7	11
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-119	15
β-strand	125-132	8	11
β-strand	137-142	6	11
β-strand	148-150	3	11
β-strand	153-156	4	9
α-helix	160-168	9
α-helix	177-192	16
β-strand	202-208	7	9
β-strand	213-220	8	9
α-helix	225-228	4
β-strand	241-247	7	12
α-helix	251-253	3

Chain 3: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	12-17	6	12
β-strand	20-25	6	12
β-strand	29-31	3	15
β-strand	34-37	4	15
β-strand	43-46	4	16
β-strand	49-52	4	16
α-helix	57-77	21
α-helix	81-83	3
α-helix	84-95	12
β-strand	108-112	5	16
β-strand	119-123	5	16
β-strand	136-139	4	12
α-helix	143-145	3
α-helix	146-151	6
α-helix	160-173	14
β-strand	178	1	17
β-strand	185-191	7	12
β-strand	195-200	6	12

Chain 4: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	20
β-strand	13-17	5	20
β-strand	18	1	21
β-strand	21-23	3	22
β-strand	26-29	4	22
β-strand	35-39	5	23
β-strand	42-48	7	23
α-helix	52-71	20
α-helix	74-76	3
α-helix	77-92	16
β-strand	100-107	8	23
β-strand	114-119	6	23
β-strand	125-127	3	23
β-strand	130-133	4	20
α-helix	137-139	3
α-helix	140-144	5
α-helix	154-171	18
β-strand	179	1	21
β-strand	182-184	3	20
β-strand	189-191	3	20

Chain 5: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	77-82	6	29
β-strand	87-91	5	29
β-strand	95-97	3	30
β-strand	100-103	4	30
β-strand	109-110	2	31
β-strand	118-119	2	31
α-helix	124-145	22
α-helix	148-150	3
α-helix	151-164	14
β-strand	173-178	6	32
β-strand	186-191	6	32
β-strand	196-197	2	32
β-strand	201-205	5	29
α-helix	211-218	8
α-helix	225-242	18
β-strand	249-255	7	29
β-strand	260-267	8	29
α-helix	268-278	11

Chain 6: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	36
β-strand	40-45	6	36
β-strand	48-50	3	37
β-strand	53-56	4	37
β-strand	62-66	5	38
β-strand	69-75	7	38
α-helix	77-97	21
α-helix	101-103	3
α-helix	105-117	13
β-strand	126-133	8	38
β-strand	139-144	6	38
β-strand	150-152	3	38
β-strand	155-159	5	36
α-helix	162-165	4
α-helix	166-169	4
β-strand	179	1	39
β-strand	188	1	39
α-helix	189-191	3
α-helix	196-213	18
β-strand	214	1	40
β-strand	221-226	6	36
β-strand	231-236	6	36

Chain 7: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	45-48	4	44
β-strand	52-58	7	44
β-strand	59	1	45
β-strand	63	1	46
β-strand	66	1	46
β-strand	73	1	45
β-strand	75-78	4	47
β-strand	82-88	7	47
α-helix	90-108	19
α-helix	120-121	2
α-helix	122-138	17
β-strand	145-152	8	47
β-strand	158-163	6	47
β-strand	171	1	47
β-strand	174-176	3	44
α-helix	178-180	3
α-helix	184-191	8
α-helix	195-197	3
α-helix	203-220	18
β-strand	228-234	7	44
β-strand	239-245	7	44
α-helix	253-256	4

Chain a: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	83
β-strand	52-58	7	83
β-strand	60	1	84
β-strand	63	1	4
β-strand	66	1	4
β-strand	70	1	84
β-strand	75-78	4	85
β-strand	82-88	7	85
α-helix	90-108	19
α-helix	122-138	17
β-strand	145-152	8	85
β-strand	158-163	6	85
β-strand	171	1	85
β-strand	175-177	3	83
α-helix	178-181	4
α-helix	184-188	5
α-helix	195-197	3
α-helix	203-220	18
β-strand	221	1	2
β-strand	227-234	8	83
β-strand	239-246	8	83
α-helix	253-256	4

39 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-1	1, b	protein	215	Saccharomyces cerevisiae S288c	P38624 (AlphaFold model)
Proteasome subunit beta type-2	2, i	protein	261	Saccharomyces cerevisiae S288c	P25043 (AlphaFold model)
Proteasome subunit beta type-3	3, h	protein	205	Saccharomyces cerevisiae S288c	P25451 (AlphaFold model)
Proteasome subunit beta type-4	4, g	protein	198	Saccharomyces cerevisiae S288c	P22141 (AlphaFold model)
Proteasome subunit beta type-5	5, f	protein	287	Saccharomyces cerevisiae S288c	P30656
Proteasome subunit beta type-6	6, e	protein	241	Saccharomyces cerevisiae S288c	P23724
Proteasome subunit beta type-7	7, a	protein	266	Saccharomyces cerevisiae S288c	P30657
Proteasome subunit alpha type-1	A, c	protein	252	Saccharomyces cerevisiae S288c	P21243
Proteasome subunit alpha type-2	B, j	protein	250	Saccharomyces cerevisiae S288c	P23639
Proteasome subunit alpha type-3	C, d	protein	258	Saccharomyces cerevisiae S288c	P23638
Proteasome subunit alpha type-4	D, n	protein	254	Saccharomyces cerevisiae S288c	P40303
Proteasome subunit alpha type-5	E, m	protein	260	Saccharomyces cerevisiae S288c	P32379

21 more molecules are not listed.

Sequence of entity 1 (1, b), FASTA

>6J2N_1 Proteasome subunit beta type-1 (chains 1, b)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 2 (2, i), FASTA

>6J2N_2 Proteasome subunit beta type-2 (chains 2, i)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 3 (3, h), FASTA

>6J2N_3 Proteasome subunit beta type-3 (chains 3, h)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 4 (4, g), FASTA

>6J2N_4 Proteasome subunit beta type-4 (chains 4, g)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 5 (5, f), FASTA

>6J2N_5 Proteasome subunit beta type-5 (chains 5, f)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Sequence of entity 6 (6, e), FASTA

>6J2N_6 Proteasome subunit beta type-6 (chains 6, e)
MATIASEYSSEASNTPIEHQFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEP
KVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKR
FFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYE
PGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKR
D

Sequence of entity 7 (7, a), FASTA

>6J2N_7 Proteasome subunit beta type-7 (chains 7, a)
MNHDPFSWGRPADSTYGAYNTQIANAGASPMVNTQQPIVTGTSVISMKYDNGVIIAADNL
GSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEAL
EPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFG
AHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTGLT
FKKNLQVENMKWDFAKDIKGYGTQKI

Sequence of entity 8 (A, c), FASTA

>6J2N_8 Proteasome subunit alpha type-1 (chains A, c)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 9 (B, j), FASTA

>6J2N_9 Proteasome subunit alpha type-2 (chains B, j)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 10 (C, d), FASTA

>6J2N_10 Proteasome subunit alpha type-3 (chains C, d)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 11 (D, n), FASTA

>6J2N_11 Proteasome subunit alpha type-4 (chains D, n)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 12 (E, m), FASTA

>6J2N_12 Proteasome subunit alpha type-5 (chains E, m)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Primary citation

Structural Snapshots of 26S Proteasome Reveal Tetraubiquitin-Induced Conformations. Ding, Z., Xu, C., Sahu, I. et al. Mol Cell (2019) 73:1150. DOI 10.1016/j.molcel.2019.01.018 · PubMed

Other PDB entries of the same protein (UniProt P38624 (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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