6J2Q: Yeast proteasome in Ub-accepted state

Yeast proteasome in Ub-accepted state (C1-b). Determined by electron microscopy at 3.8 Å resolution. Released 13 Mar 2019.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 47
Atoms: 106,311
Mol. weight: 1692.66 kDa
Released: 13 Mar 2019

Explore 6J2Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J2Q contains 594 α-helices and 576 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: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	22-26	5	2
β-strand	31-36	6	2
β-strand	39-40	2	3
β-strand	45-47	3	3
β-strand	54-55	2	4
β-strand	60-66	7	4
β-strand	67	1	1
α-helix	68-84	17
α-helix	85-89	5
α-helix	94-107	14
β-strand	114-120	7	4
β-strand	128-132	5	4
β-strand	139-141	3	4
β-strand	143-146	4	2
α-helix	149-152	4
α-helix	154-159	6
α-helix	167-183	17
β-strand	185	1	5
β-strand	192-197	6	2
β-strand	202-206	5	2
α-helix	209-212	4

Chain 2: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	11
β-strand	40-46	7	11
β-strand	49	1	12
β-strand	54	1	13
β-strand	57	1	12
β-strand	63-67	5	14
β-strand	70-76	7	14
α-helix	78-99	22
α-helix	105-118	14
β-strand	125-133	9	14
β-strand	136-142	7	14
β-strand	148-150	3	14
β-strand	153-157	5	11
α-helix	160-167	8
α-helix	177-194	18
β-strand	195	1	15
β-strand	202-208	7	11
β-strand	213-220	8	11
α-helix	225-228	4
α-helix	233-235	3
β-strand	241-247	7	16

Chain 3: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	11-16	6	16
β-strand	21-26	6	16
β-strand	29-31	3	19
β-strand	34-37	4	19
β-strand	43-46	4	20
β-strand	49-52	4	20
β-strand	55	1	21
α-helix	57-78	22
α-helix	81-83	3
α-helix	84-95	12
β-strand	105	1	21
β-strand	108-112	5	20
β-strand	119-121	3	20
β-strand	122-123	2	22
β-strand	131-132	2	22
β-strand	136-140	5	16
α-helix	143-153	11
α-helix	160-175	16
β-strand	178	1	23
β-strand	185-190	6	16
β-strand	195-200	6	16

Chain 4: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	26
β-strand	13-17	5	26
β-strand	18	1	27
β-strand	22	1	28
β-strand	27	1	28
β-strand	36-39	4	29
β-strand	42-45	4	29
β-strand	48	1	30
α-helix	53-70	18
α-helix	74-76	3
α-helix	77-91	15
β-strand	100	1	30
β-strand	102-108	7	29
β-strand	113-119	7	29
β-strand	125-127	3	29
β-strand	130-133	4	26
α-helix	136-143	8
α-helix	154-168	15
β-strand	174	1	31
β-strand	179	1	27
β-strand	181-184	4	26
β-strand	189-192	4	26

Chain 5: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	77-82	6	38
β-strand	87-92	6	38
β-strand	95-97	3	39
β-strand	100-103	4	39
β-strand	121-122	2	40
α-helix	124-145	22
α-helix	148-150	3
α-helix	151-164	14
β-strand	172-179	8	40
β-strand	185-191	7	40
β-strand	196	1	40
β-strand	199	1	40
β-strand	202-205	4	38
α-helix	208-218	11
α-helix	225-242	18
β-strand	243	1	41
β-strand	250-256	7	38
β-strand	259-266	8	38
α-helix	268-270	3
α-helix	272-278	7

Chain 6: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	45
β-strand	40-45	6	45
β-strand	48-50	3	46
β-strand	53-56	4	46
β-strand	62-64	3	47
β-strand	70-75	6	47
α-helix	77-97	21
α-helix	105-117	13
β-strand	126-131	6	47
β-strand	133	1	48
β-strand	139	1	48
β-strand	141-142	2	49
β-strand	143	1	47
β-strand	152-153	2	49
β-strand	155-158	4	45
α-helix	162-164	3
α-helix	166-172	7
β-strand	179	1	50
β-strand	188	1	50
α-helix	189-191	3
α-helix	196-213	18
β-strand	214	1	51
β-strand	221-226	6	45
β-strand	231-236	6	45

Chain 7: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	39-40	2	57
β-strand	45-48	4	58
β-strand	52-58	7	58
β-strand	62-63	2	57
β-strand	66	1	57
β-strand	75-77	3	59
β-strand	82-87	6	59
α-helix	91-108	18
α-helix	122-138	17
β-strand	146-152	7	59
β-strand	158-164	7	59
β-strand	170-171	2	59
β-strand	174-175	2	58
α-helix	178-182	5
α-helix	184-188	5
α-helix	195-197	3
α-helix	203-220	18
β-strand	227-234	8	58
β-strand	239-241	3	58
β-strand	245-246	2	58
α-helix	253-255	3

Chain a: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	39-40	2	5
β-strand	45-48	4	95
β-strand	52-58	7	95
β-strand	62-63	2	5
β-strand	66	1	5
β-strand	75-77	3	96
β-strand	82-88	7	96
β-strand	89	1	5
α-helix	90-108	19
α-helix	122-138	17
β-strand	145-152	8	96
β-strand	158-164	7	96
β-strand	170	1	96
β-strand	174-175	2	95
α-helix	178-182	5
α-helix	184-191	8
α-helix	195-197	3
α-helix	203-220	18
β-strand	227-234	8	95
β-strand	239-241	3	95
β-strand	245-246	2	95
α-helix	253-255	3

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

>6J2Q_1 Proteasome subunit beta type-1 (chains 1, b)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 2 (2, i), FASTA

>6J2Q_2 Proteasome subunit beta type-2 (chains 2, i)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 3 (3, h), FASTA

>6J2Q_3 Proteasome subunit beta type-3 (chains 3, h)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 4 (4, g), FASTA

>6J2Q_4 Proteasome subunit beta type-4 (chains 4, g)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 5 (5, f), FASTA

>6J2Q_5 Proteasome subunit beta type-5 (chains 5, f)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Sequence of entity 6 (6, e), FASTA

>6J2Q_6 Proteasome subunit beta type-6 (chains 6, e)
MATIASEYSSEASNTPIEHQFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEP
KVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKR
FFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYE
PGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKR
D

Sequence of entity 7 (7, a), FASTA

>6J2Q_7 Proteasome subunit beta type-7 (chains 7, a)
MNHDPFSWGRPADSTYGAYNTQIANAGASPMVNTQQPIVTGTSVISMKYDNGVIIAADNL
GSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEAL
EPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFG
AHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTGLT
FKKNLQVENMKWDFAKDIKGYGTQKI

Sequence of entity 8 (A, c), FASTA

>6J2Q_8 Proteasome subunit alpha type-1 (chains A, c)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 9 (B, j), FASTA

>6J2Q_9 Proteasome subunit alpha type-2 (chains B, j)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 10 (C, d), FASTA

>6J2Q_10 Proteasome subunit alpha type-3 (chains C, d)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 11 (D, n), FASTA

>6J2Q_11 Proteasome subunit alpha type-4 (chains D, n)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 12 (E, m), FASTA

>6J2Q_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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