6EF1: Yeast 26S proteasome

Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state). Determined by electron microscopy at 4.73 Å resolution. Released 17 Oct 2018.

Method: Electron microscopy
Resolution: 4.73 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 14
Atoms: 23,658
Mol. weight: 369.08 kDa
Ligands: ATP, ADP
Released: 17 Oct 2018

Explore 6EF1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EF1 contains 152 α-helices and 142 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: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	19-20	2
α-helix	26-35	10
β-strand	42-46	5	1
β-strand	51-56	6	1
β-strand	64	1	2
β-strand	80	1	3
β-strand	83	1	3
α-helix	87-108	22
α-helix	114-129	16
β-strand	131	1	4
β-strand	141-145	5	3
β-strand	153-157	5	3
β-strand	163-164	2	3
β-strand	169-171	3	1
α-helix	175-189	15
α-helix	199-201	3
α-helix	203-213	11
α-helix	215-217	3
β-strand	223-229	7	1
β-strand	232-235	4	1
α-helix	238-245	8
α-helix	246-249	4

Chain B: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	5
β-strand	13	1	6
β-strand	16	1	6
α-helix	19-22	4
α-helix	24-30	7
β-strand	34-37	4	7
β-strand	43-47	5	7
β-strand	64-68	5	8
β-strand	71-74	4	8
β-strand	77	1	9
α-helix	80-92	13
α-helix	93-98	6
α-helix	99-101	3
α-helix	104-105	2
α-helix	107-118	12
α-helix	120-123	4
β-strand	125	1	5
β-strand	127	1	4
β-strand	132	1	9
β-strand	135-137	3	8
β-strand	147-150	4	8
β-strand	156-159	4	8
β-strand	161-164	4	7
α-helix	168-178	11
α-helix	188-198	11
β-strand	211-214	4	7
α-helix	219-222	4
β-strand	235-237	3	7
α-helix	240-248	9

Chain C: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	22-28	7
α-helix	29-31	3
β-strand	34-38	5	10
β-strand	44-49	6	10
β-strand	68-70	3	11
β-strand	73-74	2	11
β-strand	76-79	4	12
β-strand	80	1	13
α-helix	85-102	18
α-helix	105-107	3
α-helix	108-111	4
α-helix	117-123	7
β-strand	125	1	14
β-strand	133-136	4	12
β-strand	139-141	3	15
β-strand	145-147	3	15
β-strand	149	1	16
β-strand	150	1	12
β-strand	159	1	16
β-strand	162-163	2	10
α-helix	169-179	11
α-helix	186-200	15
α-helix	208-210	3
β-strand	211-216	6	10
β-strand	217	1	17
β-strand	226	1	17
α-helix	232-241	10

Chain D: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	18-23	6
β-strand	34-37	4	18
β-strand	42-47	6	18
β-strand	64-66	3	19
β-strand	72-75	4	19
α-helix	80-99	20
α-helix	107-119	13
β-strand	126	1	14
β-strand	133-136	4	19
β-strand	137-138	2	20
α-helix	139	1
β-strand	145-146	2	20
β-strand	149	1	19
β-strand	157	1	19
β-strand	161-163	3	18
α-helix	168-174	7
α-helix	175-177	3
β-strand	180	1	21
β-strand	183	1	21
α-helix	188-203	16
α-helix	207-209	3
β-strand	210-215	6	18
β-strand	222	1	18
α-helix	226-237	12

Chain E: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	23-27	5
α-helix	31-33	3
β-strand	37-38	2	22
β-strand	39-40	2	23
β-strand	41-42	2	24
β-strand	45-46	2	24
β-strand	49-50	2	22
β-strand	67	1	25
β-strand	74-79	6	25
α-helix	82-102	21
α-helix	106-108	3
α-helix	109-119	11
α-helix	120-122	3
β-strand	141-146	6	25
β-strand	148	1	26
β-strand	152	1	26
β-strand	156-159	4	25
β-strand	163-166	4	25
β-strand	169-170	2	23
α-helix	176-185	10
α-helix	194-204	11
β-strand	220-223	4	24
β-strand	227-230	4	24
α-helix	233-247	15

Chain F: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	20-25	6
α-helix	27-31	5
β-strand	37-38	2	27
β-strand	39	1	28
β-strand	43-49	7	28
β-strand	52	1	29
β-strand	59	1	29
β-strand	63-67	5	30
β-strand	70-75	6	30
β-strand	77	1	31
α-helix	79-93	15
α-helix	95-99	5
α-helix	105-120	16
β-strand	131-138	8	30
β-strand	141-145	5	30
β-strand	155-156	2	30
β-strand	158-159	2	27
α-helix	166-173	8
α-helix	179-181	3
α-helix	186-197	12
α-helix	198-200	3
β-strand	211-217	7	28
α-helix	220-222	3
β-strand	223-225	3	28
α-helix	229-232	4

Chain G: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	22-31	10
β-strand	37-41	5	32
β-strand	45-50	6	32
β-strand	53-54	2	33
β-strand	59	1	30
α-helix	60	1
β-strand	68	1	34
β-strand	74-80	7	34
α-helix	84-95	12
α-helix	97-103	7
α-helix	106-108	3
α-helix	109-114	6
α-helix	119-122	4
β-strand	134-141	8	34
β-strand	146-151	6	34
β-strand	157-158	2	34
β-strand	160	1	2
β-strand	162-164	3	32
α-helix	169-180	12
α-helix	189-203	15
α-helix	204-207	4
β-strand	211-212	2	33
β-strand	215-220	6	32
β-strand	229-230	2	32
α-helix	234-247	14

Chain H: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	219-230	12
α-helix	232-238	7
β-strand	245-246	2	35
β-strand	248-249	2	36
α-helix	256-267	12
α-helix	276-279	4
α-helix	288-298	11
β-strand	306	1	35
α-helix	329-343	15
β-strand	351-352	2	35
β-strand	375-376	2	36
α-helix	379-381	3
α-helix	382-392	11
β-strand	398	1	37
α-helix	405-408	4
α-helix	417-433	17
β-strand	438	1	37
α-helix	441-452	12

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	239	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	238	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23638 (AlphaFold model)
Proteasome subunit alpha type-4	D	protein	234	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	E	protein	242	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32379
Proteasome subunit alpha type-6	F	protein	233	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40302
Probable proteasome subunit alpha type-7	G	protein	243	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21242
26S proteasome regulatory subunit 7 homolog	H	protein	262	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	273	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q01939
26S proteasome regulatory subunit 6B homolog	K	protein	276	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33298
26S proteasome subunit RPT4	L	protein	271	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53549

2 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6EF1_1 Proteasome subunit alpha type-1 (chains A)
DRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSYI
FCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRA
YMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKID
HINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVAIAEQ

Sequence of entity 2 (B), FASTA

>6EF1_2 Proteasome subunit alpha type-2 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C), FASTA

>6EF1_3 Proteasome subunit alpha type-3 (chains C)
SRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLY
KLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGG
LRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVD
DAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTGIT

Sequence of entity 4 (D), FASTA

>6EF1_4 Proteasome subunit alpha type-4 (chains D)
SIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKID
SHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRP
FGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATV
EECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQE

Sequence of entity 5 (E), FASTA

>6EF1_5 Proteasome subunit alpha type-5 (chains E)
DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIV
EIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGAS
GEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWH
SSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKEA
AE

Sequence of entity 6 (F), FASTA

>6EF1_6 Proteasome subunit alpha type-6 (chains F)
FRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQK
KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQ
SYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIK
IDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G), FASTA

>6EF1_7 Probable proteasome subunit alpha type-7 (chains G)
TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV
KIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTL
YNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPE
GLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFAQK
EIN

Sequence of entity 8 (H), FASTA

>6EF1_8 26S proteasome regulatory subunit 7 homolog (chains H)
SVTMMTVEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPG
TGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDA
VGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDR
KVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRA
RRKVATEKDFLKAVDKVISGYK

Sequence of entity 9 (I), FASTA

>6EF1_9 26S proteasome regulatory subunit 4 homolog (chains I)
MVSVMKMDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPG
TGKTLLAKAVANQTSATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDA
IGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDR
KILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTEAGLLALRE
RRMQVTAEDFKQAKERVMKNKVEENLEGLYL

Sequence of entity 10 (J), FASTA

>6EF1_10 26S proteasome regulatory subunit 8 homolog (chains J)
LVSLMMVEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPG
TGKTLLARAVAHHTDCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDS
IGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDR
KIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTEAGMYALRE
RRIHVTQEDFELAVGKVMNKNQETAISVAKLFK

Sequence of entity 11 (K), FASTA

>6EF1_11 26S proteasome regulatory subunit 6B homolog (chains K)
DSDSSISVMGENEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLY
GPPGTGKTMLVKAVANSTKAAFIRVNGSEFVHKYLGEGPRMVRDVFRLARENAPSIIFID
EVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPG
RLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGL
RAVRKNRYVILQSDLEEAYATQVKTDNTVDKFDFYK

Sequence of entity 12 (L), FASTA

>6EF1_12 26S proteasome subunit RPT4 (chains L)
LVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPG
TGKTLLAKAVAATIGANFIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEVDA
IGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDR
KVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATEAGFFAIRD
DRDHINPDDLMKAVRKVAEVKKLEGTIEYQK

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

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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