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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