7QO3: 26S proteasome-Ubp6 complex in the si state

Structure of the 26S proteasome-Ubp6 complex in the si state (Core Particle and Lid). Determined by electron microscopy at 6.1 Å resolution. Released 13 Apr 2022.

Method: Electron microscopy
Resolution: 6.1 Å
Organism: Saccharomyces cerevisiae
Chains: 41
Atoms: 90,281
Mol. weight: 1400.61 kDa
Released: 13 Apr 2022

Explore 7QO3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QO3 contains 466 α-helices and 454 β-strands across 41 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	108
β-strand	21-25	5	108
β-strand	29-31	3	78
β-strand	34-37	4	78
β-strand	43-45	3	109
β-strand	50-56	7	109
α-helix	58-79	22
α-helix	81-83	3
α-helix	84-96	13
β-strand	104-110	7	109
β-strand	118-122	5	109
β-strand	129-130	2	109
β-strand	133-137	5	108
α-helix	139-141	3
α-helix	144-150	7
α-helix	157-174	18
β-strand	175	1	76
β-strand	182-187	6	108
β-strand	192-197	6	108
α-helix	199-203	5

Chain 2: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	90
β-strand	40-46	7	90
β-strand	49-51	3	73
β-strand	54-57	4	73
β-strand	63-65	3	110
β-strand	71-75	5	110
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-119	15
β-strand	126-133	8	110
β-strand	136-142	7	110
β-strand	148-150	3	110
β-strand	153-157	5	90
α-helix	160-170	11
α-helix	177-194	18
β-strand	195	1	70
β-strand	202-208	7	90
β-strand	213-220	8	90
α-helix	225-228	4
β-strand	241-247	7	111

Chains 3 and j: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	11-16	6	111
β-strand	21-26	6	111
β-strand	29-31	3	66
β-strand	34-37	4	66
β-strand	43-46	4	112
β-strand	49-55	7	112
α-helix	57-78	22
α-helix	81-83	3
α-helix	84-97	14
β-strand	105-113	9	112
β-strand	118-125	8	112
β-strand	128-133	6	112
β-strand	136-140	5	111
α-helix	143-153	11
α-helix	160-176	17
β-strand	178	1	64
β-strand	185-190	6	111
β-strand	195-200	6	111
α-helix	201	1

Chains 4 and k: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	113
β-strand	12-18	7	113
β-strand	21-23	3	114
β-strand	26-29	4	114
β-strand	35-39	5	115
β-strand	42-48	7	115
α-helix	52-70	19
α-helix	74-76	3
α-helix	77-93	17
β-strand	100-108	9	115
β-strand	113-120	8	115
β-strand	124-127	4	115
β-strand	130-132	3	113
α-helix	136-147	12
α-helix	154-171	18
β-strand	179-185	7	113
β-strand	188-192	5	113

Chain 5: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	77-83	7	116
β-strand	86-91	6	116
β-strand	95-96	2	117
β-strand	100	1	56
β-strand	101-103	3	117
β-strand	109-113	5	118
β-strand	116-119	4	118
β-strand	121	1	118
α-helix	124-145	22
α-helix	148-150	3
α-helix	151-164	14
β-strand	173-180	8	118
β-strand	184-191	8	118
β-strand	196-199	4	118
β-strand	201-205	5	116
α-helix	208-217	10
α-helix	225-242	18
β-strand	249-256	8	116
β-strand	259-267	9	116
α-helix	268-279	12

Chains 6 and m: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	4
β-strand	29-34	6	4
β-strand	37-38	2	5
β-strand	42	1	48
β-strand	43-45	3	5
β-strand	52-53	2	6
β-strand	58-64	7	6
α-helix	66-86	21
α-helix	94-107	14
β-strand	115-122	8	6
β-strand	128-133	6	6
β-strand	139-142	4	6
β-strand	144-148	5	4
α-helix	151-162	12
β-strand	168	1	7
β-strand	177	1	7
α-helix	178-180	3
α-helix	185-202	18
β-strand	203	1	46
β-strand	210-216	7	4
β-strand	219-225	7	4

Chain 7: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	14
β-strand	44-48	5	15
β-strand	52-58	7	15
β-strand	61-63	3	14
β-strand	66-69	4	14
β-strand	75-78	4	14
β-strand	82-89	8	14
α-helix	90-108	19
α-helix	122-138	17
β-strand	145-152	8	14
β-strand	158-164	7	14
β-strand	170-171	2	14
β-strand	174-176	3	15
α-helix	178-181	4
α-helix	184-191	8
α-helix	198-200	3
α-helix	203-220	18
β-strand	221	1	39
β-strand	228-234	7	15
β-strand	239-245	7	15
α-helix	246-247	2

Chain a: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	26-32	7
β-strand	42-46	5	1
β-strand	51-56	6	1
β-strand	64	1	2
β-strand	72-74	3	3
β-strand	79-84	6	3
α-helix	87-108	22
α-helix	111-113	3
α-helix	114-128	15
α-helix	134-136	3
β-strand	140-146	7	3
β-strand	152-157	6	3
β-strand	163-166	4	3
β-strand	168-171	4	1
α-helix	175-189	15
α-helix	199-214	16
β-strand	223-229	7	1
β-strand	232-236	5	1
α-helix	238-250	13

28 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-1	A, a	protein	252	Saccharomyces cerevisiae	P21243 (AlphaFold model)
Proteasome subunit alpha type-2	B, b	protein	250	Saccharomyces cerevisiae	P23639 (AlphaFold model)
Proteasome subunit alpha type-3	C, c	protein	258	Saccharomyces cerevisiae	P23638 (AlphaFold model)
Proteasome subunit alpha type-4	D, d	protein	254	Saccharomyces cerevisiae	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	E, e	protein	260	Saccharomyces cerevisiae	P32379
Proteasome subunit alpha type-6	F, f	protein	234	Saccharomyces cerevisiae	P40302
Probable proteasome subunit alpha type-7	G, g	protein	288	Saccharomyces cerevisiae	P21242
Proteasome subunit beta type-1	1, h	protein	215	Saccharomyces cerevisiae	P38624
Proteasome subunit beta type-2	2, i	protein	261	Saccharomyces cerevisiae	P25043
Proteasome subunit beta type-3	3, j	protein	205	Saccharomyces cerevisiae	P25451
Proteasome subunit beta type-4	4, k	protein	198	Saccharomyces cerevisiae	P22141
Proteasome subunit beta type-5	5, l	protein	287	Saccharomyces cerevisiae	P30656

15 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA

>7QO3_1 Proteasome subunit alpha type-1 (chains A, a)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 2 (B, b), FASTA

>7QO3_2 Proteasome subunit alpha type-2 (chains B, b)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C, c), FASTA

>7QO3_3 Proteasome subunit alpha type-3 (chains C, c)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 4 (D, d), FASTA

>7QO3_4 Proteasome subunit alpha type-4 (chains D, d)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 5 (E, e), FASTA

>7QO3_5 Proteasome subunit alpha type-5 (chains E, e)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 6 (F, f), FASTA

>7QO3_6 Proteasome subunit alpha type-6 (chains F, f)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G, g), FASTA

>7QO3_7 Probable proteasome subunit alpha type-7 (chains G, g)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 8 (1, h), FASTA

>7QO3_8 Proteasome subunit beta type-1 (chains 1, h)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 9 (2, i), FASTA

>7QO3_9 Proteasome subunit beta type-2 (chains 2, i)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 10 (3, j), FASTA

>7QO3_10 Proteasome subunit beta type-3 (chains 3, j)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 11 (4, k), FASTA

>7QO3_11 Proteasome subunit beta type-4 (chains 4, k)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 12 (5, l), FASTA

>7QO3_12 Proteasome subunit beta type-5 (chains 5, l)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Primary citation

Allosteric control of Ubp6 and the proteasome via a bidirectional switch. Hung, K.Y.S., Klumpe, S., Eisele, M.R. et al. Nat Commun (2022) 13:838-838. DOI 10.1038/s41467-022-28186-y · PubMed

Other PDB entries of the same protein (UniProt P21243 (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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