6FVY: 26S proteasome, s6 state

26S proteasome, s6 state. Determined by electron microscopy at 6.1 Å resolution. Released 22 Aug 2018.

Method: Electron microscopy
Resolution: 6.1 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 47
Atoms: 110,555
Mol. weight: 1582.74 kDa
Ligands: ATP, MG, ADP
Released: 22 Aug 2018

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

Secondary structure: helices and β-sheets

6FVY contains 551 α-helices and 507 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	11-17	7	111
β-strand	20-26	7	111
β-strand	29-31	3	70
β-strand	34-37	4	70
β-strand	43-45	3	112
β-strand	50-56	7	112
α-helix	58-79	22
α-helix	81-83	3
α-helix	84-96	13
β-strand	104-111	8	112
β-strand	117-122	6	112
β-strand	129-131	3	112
β-strand	133-137	5	111
α-helix	144-150	7
α-helix	157-173	17
β-strand	175	1	68
β-strand	182-188	7	111
β-strand	192-195	4	111
α-helix	199-202	4

Chain 2: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	32-37	6	79
β-strand	40-46	7	79
β-strand	49-51	3	64
β-strand	54-57	4	64
β-strand	63-67	5	113
β-strand	70-76	7	113
α-helix	78-99	22
α-helix	105-119	15
β-strand	125-133	9	113
β-strand	136-142	7	113
β-strand	148-150	3	113
β-strand	153-156	4	79
α-helix	160-170	11
α-helix	177-194	18
β-strand	202-208	7	79
β-strand	213-220	8	79
β-strand	245-247	3	114

Chain 3: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	11-16	6	114
β-strand	21-26	6	114
β-strand	29-31	3	115
β-strand	34-37	4	115
β-strand	43-46	4	116
β-strand	49-55	7	116
α-helix	57-78	22
α-helix	81-83	3
α-helix	84-96	13
β-strand	105-112	8	116
β-strand	119-123	5	116
β-strand	131	1	116
β-strand	136-140	5	114
α-helix	143-153	11
α-helix	160-176	17
β-strand	178	1	57
β-strand	185-190	6	114
β-strand	195-199	5	114

Chain 4: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	117
β-strand	13-18	6	117
β-strand	21-23	3	118
β-strand	26-29	4	118
β-strand	35-39	5	119
β-strand	42-48	7	119
α-helix	52-71	20
α-helix	77-93	17
β-strand	100-108	9	119
β-strand	113-119	7	119
β-strand	125-127	3	119
β-strand	130-133	4	117
α-helix	136-138	3
α-helix	141-147	7
α-helix	156-170	15
β-strand	179-185	7	117
β-strand	188-192	5	117

Chain 5: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	77-83	7	120
β-strand	86-91	6	120
β-strand	95-96	2	121
β-strand	101-103	3	121
β-strand	109-113	5	122
β-strand	116-119	4	122
α-helix	124-145	22
α-helix	148-150	3
α-helix	151-164	14
β-strand	173-180	8	122
β-strand	184-191	8	122
β-strand	196-199	4	122
β-strand	201-205	5	120
α-helix	208-217	10
α-helix	225-242	18
β-strand	249-256	8	120
β-strand	259-267	9	120
α-helix	268-279	12

Chain 6: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	3
β-strand	29-34	6	3
β-strand	37-39	3	4
β-strand	42-45	4	4
β-strand	52-53	2	5
β-strand	58-64	7	5
α-helix	66-86	21
α-helix	91-93	3
α-helix	94-106	13
β-strand	115-122	8	5
β-strand	128-133	6	5
β-strand	139-141	3	5
β-strand	144-148	5	3
α-helix	151-161	11
β-strand	168	1	6
β-strand	177	1	6
α-helix	178-180	3
α-helix	185-202	18
β-strand	203	1	40
β-strand	209-217	9	3
β-strand	219-226	8	3

Chain 7: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	39-40	2	11
β-strand	44-48	5	12
β-strand	52-58	7	12
β-strand	60-63	4	11
β-strand	66-70	5	11
β-strand	75-78	4	13
β-strand	82-88	7	13
β-strand	89	1	11
α-helix	91-108	18
α-helix	122-137	16
β-strand	145-152	8	13
β-strand	158-164	7	13
β-strand	170	1	13
β-strand	174-176	3	12
α-helix	180-183	4
α-helix	185-191	7
α-helix	203-219	17
β-strand	221	1	33
β-strand	227-234	8	12
β-strand	238-246	9	12
α-helix	254-257	4

Chain a: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	26-30	5
α-helix	31-33	3
β-strand	42-46	5	1
β-strand	51-56	6	1
β-strand	72-76	5	2
β-strand	79-84	6	2
α-helix	87-107	21
α-helix	114-130	17
β-strand	140-147	8	2
β-strand	151-157	7	2
β-strand	163-166	4	2
β-strand	169-171	3	1
α-helix	175-189	15
α-helix	199-214	16
β-strand	223-229	7	1
β-strand	230	1	2
β-strand	232-236	5	1
α-helix	238-249	12

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 alpha type-1	A, a	protein	244	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21243 (AlphaFold model)
Proteasome subunit alpha type-2	B, b	protein	248	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23639 (AlphaFold model)
Proteasome subunit alpha type-3	C, c	protein	241	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23638 (AlphaFold model)
Proteasome subunit alpha type-4	D, d	protein	252	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	E, e	protein	245	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32379
Proteasome subunit alpha type-6	F, f	protein	232	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40302
Probable proteasome subunit alpha type-7	G, g	protein	245	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21242
Proteasome subunit beta type-1	1, h	protein	196	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38624
Proteasome subunit beta type-2	2, i	protein	226	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25043
Proteasome subunit beta type-3	3, j	protein	204	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25451
Proteasome subunit beta type-4	4, k	protein	195	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22141
Proteasome subunit beta type-5	5, l	protein	212	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P30656

21 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA

>6FVY_1 Proteasome subunit alpha type-1 (chains A, a)
SAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPT
TVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQI
YTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFK
KSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVA
IAEQ

Sequence of entity 2 (B, b), FASTA

>6FVY_2 Proteasome subunit alpha type-2 (chains B, b)
DRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLS
KVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEAT
QSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDE
LELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQE
INDRLEAL

Sequence of entity 3 (C, c), FASTA

>6FVY_3 Proteasome subunit alpha type-3 (chains C, c)
RYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTE
KLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQ
HGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDM
KVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTGI
T

Sequence of entity 4 (D, d), FASTA

>6FVY_4 Proteasome subunit alpha type-4 (chains D, d)
GYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPS
KVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQ
SGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRK
EPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQE
QQEQDKKKKSNH

Sequence of entity 5 (E, e), FASTA

>6FVY_5 Proteasome subunit alpha type-5 (chains E, e)
SEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIE
KIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGE
GASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLN
EWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKE
KEAAE

Sequence of entity 6 (F, f), FASTA

>6FVY_6 Proteasome subunit alpha type-6 (chains F, f)
RNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKK
IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS
YGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKI
DGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G, g), FASTA

>6FVY_7 Probable proteasome subunit alpha type-7 (chains G, g)
IGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQK
NVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAH
TLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHH
PEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFA
QKEIN

Sequence of entity 8 (1, h), FASTA

>6FVY_8 Proteasome subunit beta type-1 (chains 1, h)
TSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQ
YHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVH
KLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTA
AGVERLIFYPDEYEQL

Sequence of entity 9 (2, i), FASTA

>6FVY_9 Proteasome subunit beta type-2 (chains 2, i)
TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIG
SNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTD
VGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEI
GKDAEYLRNYLTPNVREEKQKSYKFPRGTTAVLKESIVNICDIQEE

Sequence of entity 10 (3, j), FASTA

>6FVY_10 Proteasome subunit beta type-3 (chains 3, j)
SDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVT
TLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFI
AGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALS
GWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 11 (4, k), FASTA

>6FVY_11 Proteasome subunit beta type-4 (chains 4, k)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDF

Sequence of entity 12 (5, l), FASTA

>6FVY_12 Proteasome subunit beta type-5 (chains 5, l)
TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLG
SQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGT
RLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHV
TEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
MG	Magnesium ion	Mg	6
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

Primary citation

Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating. Eisele, M.R., Reed, R.G., Rudack, T. et al. Cell Rep (2018) 24:1301-1315.e5. DOI 10.1016/j.celrep.2018.07.004 · 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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