6EF0: Yeast 26S proteasome

Yeast 26S proteasome bound to ubiquitinated substrate (1D* motor state). Determined by electron microscopy at 4.43 Å resolution. Released 17 Oct 2018.

Method: Electron microscopy
Resolution: 4.43 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 14
Atoms: 24,748
Mol. weight: 370.67 kDa
Ligands: ADP, ATP
Released: 17 Oct 2018

Explore 6EF0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EF0 contains 142 α-helices and 147 β-strands across 13 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: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	28-34	7
β-strand	42-45	4	1
β-strand	52-55	4	1
β-strand	64	1	2
β-strand	72	1	3
β-strand	79-80	2	4
β-strand	82	1	3
β-strand	83	1	4
α-helix	88-108	21
α-helix	111-113	3
α-helix	114-117	4
α-helix	123-127	5
β-strand	131	1	5
α-helix	135-137	3
β-strand	141-146	6	4
β-strand	152-157	6	4
β-strand	164-166	3	4
β-strand	171	1	1
α-helix	183-186	4
α-helix	201-214	14
β-strand	226	1	1
β-strand	227-229	3	6
β-strand	232-234	3	6
α-helix	239-244	6

Chain B: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
β-strand	34-38	5	7
β-strand	43-48	6	7
β-strand	56	1	4
β-strand	65-68	4	8
β-strand	71-74	4	8
α-helix	83-92	10
α-helix	93-99	7
α-helix	100-101	2
α-helix	104-105	2
α-helix	110-119	10
β-strand	127	1	5
α-helix	128-130	3
β-strand	135-138	4	8
β-strand	146-149	4	8
α-helix	156-157	2
β-strand	158	1	8
β-strand	161-164	4	7
α-helix	168-178	11
α-helix	185-197	13
α-helix	206-208	3
β-strand	209-214	6	7
β-strand	235-237	3	7

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	21-28	8
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	44-49	6	9
β-strand	68	1	10
β-strand	74-75	2	10
β-strand	78-79	2	11
β-strand	80	1	12
α-helix	81-83	3
α-helix	87-102	16
α-helix	112-122	11
β-strand	125	1	13
α-helix	128-131	4
β-strand	133-134	2	11
β-strand	136	1	14
β-strand	137-138	2	10
β-strand	139-140	2	15
β-strand	146-147	2	15
β-strand	149-150	2	14
β-strand	158-159	2	14
β-strand	160	1	16
β-strand	163-164	2	9
α-helix	170-176	7
α-helix	190-197	8
α-helix	208-210	3
β-strand	212	1	9
β-strand	214-216	3	9
β-strand	228-229	2	9
α-helix	232-241	10

Chain D: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	17
β-strand	17	1	17
α-helix	18-26	9
α-helix	27-29	3
β-strand	33-37	5	18
β-strand	42-45	4	18
β-strand	55	1	16
β-strand	66	1	19
β-strand	72-74	3	19
β-strand	77	1	20
α-helix	82-99	18
α-helix	109-119	11
β-strand	126	1	13
β-strand	131	1	20
β-strand	133-136	4	19
α-helix	138-139	2
β-strand	147-150	4	19
β-strand	156-158	3	19
β-strand	161-164	4	18
α-helix	172-178	7
α-helix	188-199	12
α-helix	200-202	3
β-strand	212-215	4	18
α-helix	217-219	3
β-strand	222-223	2	18
α-helix	226-238	13

Chain E: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	22-29	8
β-strand	37-40	4	21
β-strand	46-51	6	21
β-strand	67-69	3	22
β-strand	74-77	4	22
α-helix	86-102	17
α-helix	110-117	8
α-helix	119-121	3
β-strand	143-146	4	22
β-strand	154-155	2	22
β-strand	157	1	23
β-strand	165	1	23
β-strand	169-171	3	21
α-helix	177-184	8
α-helix	193-207	15
β-strand	215	1	21
β-strand	217-223	7	21
β-strand	227-230	4	21
α-helix	233-239	7
α-helix	241-247	7

Chain F: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	20-31	12
β-strand	35-39	5	24
β-strand	43-49	7	24
β-strand	63-67	5	25
β-strand	70-73	4	25
β-strand	76	1	26
α-helix	79-94	16
α-helix	102-104	3
α-helix	106-118	13
β-strand	130	1	26
β-strand	133-138	6	25
β-strand	141-146	6	25
β-strand	154-155	2	25
β-strand	156	1	27
β-strand	159	1	24
α-helix	166-174	9
α-helix	186-195	10
β-strand	211-217	7	24
β-strand	223-225	3	24
α-helix	227-229	3
α-helix	231-233	3

Chain G: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	28
β-strand	20	1	28
α-helix	27-32	6
β-strand	37-41	5	29
β-strand	45-52	8	29
β-strand	59	1	27
β-strand	67-69	3	30
β-strand	75-77	3	30
β-strand	79	1	31
β-strand	81	1	31
α-helix	83-103	21
α-helix	109-119	11
α-helix	121-123	3
β-strand	137-139	3	30
β-strand	141-142	2	32
β-strand	145-146	2	32
β-strand	149-150	2	30
β-strand	159	1	30
β-strand	160	1	2
β-strand	162	1	29
α-helix	166-168	3
α-helix	169-180	12
α-helix	189-203	15
α-helix	204-207	4
β-strand	213-216	4	29
β-strand	218	1	33
β-strand	219-220	2	29
α-helix	221-224	4
β-strand	229	1	33
α-helix	234-245	12

Chain H: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	216-224	9
α-helix	233-236	4
β-strand	246-248	3	34
α-helix	256-264	9
α-helix	266-268	3
β-strand	270	1	35
α-helix	276-279	4
α-helix	287-298	12
β-strand	304	1	35
β-strand	305-306	2	36
α-helix	312-316	5
α-helix	319-321	3
α-helix	328-340	13
β-strand	350-351	2	36
β-strand	373-375	3	34
α-helix	382-386	5
β-strand	398	1	37
α-helix	406-409	4
α-helix	419-426	8
α-helix	429-433	5
β-strand	438	1	37
α-helix	441-450	10

5 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	protein	238	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21243 (AlphaFold model)
Proteasome subunit alpha type-2	B	protein	250	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23639 (AlphaFold model)
Proteasome subunit alpha type-3	C	protein	244	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23638 (AlphaFold model)
Proteasome subunit alpha type-4	D	protein	242	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	E	protein	249	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32379
Proteasome subunit alpha type-6	F	protein	234	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40302
Probable proteasome subunit alpha type-7	G	protein	246	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21242
26S proteasome regulatory subunit 7 homolog	H	protein	257	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33299
26S proteasome regulatory subunit 4 homolog	I	protein	271	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40327
26S proteasome regulatory subunit 8 homolog	J	protein	276	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q01939
26S proteasome regulatory subunit 6B homolog	K	protein	272	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33298
26S proteasome subunit RPT4	L	protein	273	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53549

2 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6EF0_1 Proteasome subunit alpha type-1 (chains A)
GYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVS
YIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQ
RAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSK
IDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVAI

Sequence of entity 2 (B), FASTA

>6EF0_2 Proteasome subunit alpha type-2 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C), FASTA

>6EF0_3 Proteasome subunit alpha type-3 (chains C)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGI

Sequence of entity 4 (D), FASTA

>6EF0_4 Proteasome subunit alpha type-4 (chains D)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QE

Sequence of entity 5 (E), FASTA

>6EF0_5 Proteasome subunit alpha type-5 (chains E)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAA

Sequence of entity 6 (F), FASTA

>6EF0_6 Proteasome subunit alpha type-6 (chains F)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G), FASTA

>6EF0_7 Probable proteasome subunit alpha type-7 (chains G)
SIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQ
KNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQA
HTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDH
HPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDF
AQKEIN

Sequence of entity 8 (H), FASTA

>6EF0_8 26S proteasome regulatory subunit 7 homolog (chains H)
EEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCA
RAVANRTDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFD
DGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLP
DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATE
KDFLKAVDKVISGYKKF

Sequence of entity 9 (I), FASTA

>6EF0_9 26S proteasome regulatory subunit 4 homolog (chains I)
PMVSVMKMDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAP
GTGKTLLAKAVANQTSATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEID
AIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRID
RKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTEAGLLALR
ERRMQVTAEDFKQAKERVMKNKVEENLEGLY

Sequence of entity 10 (J), FASTA

>6EF0_10 26S proteasome regulatory subunit 8 homolog (chains J)
ADPLVSLMMVEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYG
PPGTGKTLLARAVAHHTDCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDE
IDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGR
IDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTEAGMYA
LRERRIHVTQEDFELAVGKVMNKNQETAISVAKLFK

Sequence of entity 11 (K), FASTA

>6EF0_11 26S proteasome regulatory subunit 6B homolog (chains K)
SISVMGENEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPG
TGKTMLVKAVANSTKAAFIRVNGSEFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDS
IATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDR
KIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVR
KNRYVILQSDLEEAYATQVKTDNTVDKFDFYK

Sequence of entity 12 (L), FASTA

>6EF0_12 26S proteasome subunit RPT4 (chains L)
DPLVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGP
PGTGKTLLAKAVAATIGANFIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEV
DAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRL
DRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATEAGFFAI
RDDRDHINPDDLMKAVRKVAEVKKLEGTIEYQK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3

Primary citation

Substrate-engaged 26Sproteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation. de la Pena, A.H., Goodall, E.A., Gates, S.N. et al. Science (2018) 362. DOI 10.1126/science.aav0725 · 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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