7QO6: BJ4_G0020160.mRNA.1.CDS.1
26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state. Determined by electron microscopy at 6.3 Å resolution. Released 16 Mar 2022.
- Method
- Electron microscopy
- Resolution
- 6.3 Å
- Organisms
- Saccharomyces cerevisiae, Homo sapiens
- Chains
- 49
- Atoms
- 112,930
- Mol. weight
- 1761.62 kDa
- Ligands
- ATP, MG, ADP
- Released
- 16 Mar 2022
Explore 7QO6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7QO6 contains 575 α-helices and 550 β-strands across 49 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.
Chains 1 and h: 6 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-17 | 7 | 116 |
| β-strand | 20-26 | 7 | 116 |
| β-strand | 29-31 | 3 | 74 |
| β-strand | 34-37 | 4 | 74 |
| β-strand | 43-45 | 3 | 117 |
| β-strand | 50-56 | 7 | 117 |
| α-helix | 58-79 | 22 | |
| α-helix | 81-83 | 3 | |
| α-helix | 84-97 | 14 | |
| β-strand | 104-112 | 9 | 117 |
| β-strand | 116-122 | 7 | 117 |
| β-strand | 129-131 | 3 | 117 |
| β-strand | 133-137 | 5 | 116 |
| α-helix | 144-150 | 7 | |
| α-helix | 157-174 | 18 | |
| β-strand | 175 | 1 | 72 |
| β-strand | 182-188 | 7 | 116 |
| β-strand | 192-197 | 6 | 116 |
| α-helix | 199-203 | 5 | |
Chain 2: 5 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-37 | 7 | 84 |
| β-strand | 40-46 | 7 | 84 |
| β-strand | 49-51 | 3 | 69 |
| β-strand | 54-57 | 4 | 69 |
| β-strand | 63-67 | 5 | 124 |
| β-strand | 70-76 | 7 | 124 |
| α-helix | 78-99 | 22 | |
| α-helix | 105-117 | 13 | |
| β-strand | 125-133 | 9 | 124 |
| β-strand | 136-142 | 7 | 124 |
| β-strand | 148-150 | 3 | 124 |
| β-strand | 153-157 | 5 | 84 |
| α-helix | 160-170 | 11 | |
| α-helix | 177-194 | 18 | |
| β-strand | 202-208 | 7 | 84 |
| β-strand | 213-220 | 8 | 84 |
| α-helix | 224-228 | 5 | |
| β-strand | 241-247 | 7 | 125 |
Chain 3: 7 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| β-strand | 11-16 | 6 | 125 |
| β-strand | 21-26 | 6 | 125 |
| β-strand | 29-30 | 2 | 128 |
| β-strand | 35-37 | 3 | 128 |
| β-strand | 43-46 | 4 | 129 |
| β-strand | 49-55 | 7 | 129 |
| α-helix | 57-78 | 22 | |
| α-helix | 81-83 | 3 | |
| α-helix | 84-97 | 14 | |
| β-strand | 105-112 | 8 | 129 |
| β-strand | 119-125 | 7 | 129 |
| β-strand | 128-132 | 5 | 129 |
| β-strand | 136-140 | 5 | 125 |
| α-helix | 143-153 | 11 | |
| α-helix | 160-176 | 17 | |
| β-strand | 178 | 1 | 63 |
| β-strand | 185-190 | 6 | 125 |
| β-strand | 195-200 | 6 | 125 |
| α-helix | 201 | 1 | |
Chains 4 and k: 4 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 130 |
| β-strand | 12-18 | 7 | 130 |
| β-strand | 21-23 | 3 | 131 |
| β-strand | 26-29 | 4 | 131 |
| β-strand | 35-39 | 5 | 132 |
| β-strand | 42-48 | 7 | 132 |
| α-helix | 52-70 | 19 | |
| α-helix | 77-93 | 17 | |
| β-strand | 100-108 | 9 | 132 |
| β-strand | 113-119 | 7 | 132 |
| β-strand | 125-127 | 3 | 132 |
| β-strand | 130-132 | 3 | 130 |
| α-helix | 134-147 | 14 | |
| α-helix | 154-171 | 18 | |
| β-strand | 174 | 1 | 59 |
| β-strand | 179-185 | 7 | 130 |
| β-strand | 188-192 | 5 | 130 |
Chains 5 and l: 6 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 77-83 | 7 | 133 |
| β-strand | 86-92 | 7 | 133 |
| β-strand | 95-97 | 3 | 54 |
| β-strand | 100-103 | 4 | 54 |
| β-strand | 109-113 | 5 | 134 |
| β-strand | 116-119 | 4 | 134 |
| β-strand | 121 | 1 | 134 |
| α-helix | 124-145 | 22 | |
| α-helix | 148-150 | 3 | |
| α-helix | 151-164 | 14 | |
| β-strand | 173-180 | 8 | 134 |
| β-strand | 184-191 | 8 | 134 |
| β-strand | 196-199 | 4 | 134 |
| β-strand | 201-205 | 5 | 133 |
| α-helix | 208-217 | 10 | |
| α-helix | 225-242 | 18 | |
| β-strand | 249-256 | 8 | 133 |
| β-strand | 259-267 | 9 | 133 |
| α-helix | 268-279 | 12 | |
Chains 6 and m: 6 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 19-24 | 6 | 4 |
| β-strand | 29-34 | 6 | 4 |
| β-strand | 37-39 | 3 | 5 |
| β-strand | 42-45 | 4 | 5 |
| β-strand | 51-53 | 3 | 6 |
| β-strand | 58-64 | 7 | 6 |
| α-helix | 66-86 | 21 | |
| α-helix | 90-93 | 4 | |
| 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 | 151-161 | 11 | |
| β-strand | 168 | 1 | 7 |
| β-strand | 177 | 1 | 7 |
| α-helix | 178-183 | 6 | |
| α-helix | 185-202 | 18 | |
| β-strand | 203 | 1 | 45 |
| β-strand | 210-216 | 7 | 4 |
| β-strand | 219-225 | 7 | 4 |
Chain 7: 7 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40 | 1 | 13 |
| β-strand | 44-48 | 5 | 14 |
| β-strand | 52-58 | 7 | 14 |
| β-strand | 60-63 | 4 | 13 |
| β-strand | 66-70 | 5 | 13 |
| β-strand | 75-78 | 4 | 15 |
| β-strand | 82-88 | 7 | 15 |
| β-strand | 89 | 1 | 13 |
| α-helix | 90-108 | 19 | |
| α-helix | 122-139 | 18 | |
| β-strand | 145-152 | 8 | 15 |
| β-strand | 158-164 | 7 | 15 |
| β-strand | 170-171 | 2 | 15 |
| β-strand | 174-176 | 3 | 14 |
| α-helix | 178-181 | 4 | |
| α-helix | 184-191 | 8 | |
| α-helix | 195-197 | 3 | |
| α-helix | 203-220 | 18 | |
| β-strand | 221 | 1 | 39 |
| β-strand | 228-234 | 7 | 14 |
| β-strand | 238-245 | 8 | 14 |
| α-helix | 253-257 | 5 | |
Chain 8: 11 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 111 | 1 | 118 |
| α-helix | 118-128 | 11 | |
| α-helix | 131-139 | 9 | |
| α-helix | 153-172 | 20 | |
| β-strand | 179 | 1 | 118 |
| α-helix | 182-191 | 10 | |
| α-helix | 210-225 | 16 | |
| α-helix | 227-233 | 7 | |
| β-strand | 235-243 | 9 | 119 |
| β-strand | 250-253 | 4 | 119 |
| β-strand | 257-258 | 2 | 119 |
| β-strand | 261-263 | 3 | 120 |
| β-strand | 271 | 1 | 121 |
| α-helix | 273-280 | 8 | |
| β-strand | 281-286 | 6 | 119 |
| β-strand | 295-305 | 11 | 119 |
| β-strand | 311-314 | 4 | 120 |
| β-strand | 317-320 | 4 | 122 |
| β-strand | 325-328 | 4 | 122 |
| β-strand | 334 | 1 | 121 |
| β-strand | 339-340 | 2 | 120 |
| β-strand | 345 | 1 | 119 |
| α-helix | 347-375 | 29 | |
| α-helix | 402-415 | 14 | |
| β-strand | 429-439 | 11 | 120 |
| β-strand | 445 | 1 | 123 |
| β-strand | 447-453 | 7 | 120 |
| β-strand | 460-465 | 6 | 120 |
| β-strand | 468-473 | 6 | 120 |
| α-helix | 474-478 | 5 | |
| α-helix | 479-481 | 3 | |
| β-strand | 488-496 | 9 | 120 |
33 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 |
|---|
| BJ4_G0020160.mRNA.1.CDS.1 | A, a | protein | 252 | Saccharomyces cerevisiae | A0A6A5PYC9 |
| HLJ1_G0039880.mRNA.1.CDS.1 | B, b | protein | 250 | Saccharomyces cerevisiae | A0A6L1BIF8 |
| BJ4_G0021480.mRNA.1.CDS.1 | C, c | protein | 258 | Saccharomyces cerevisiae | A0A6A5PXC6 |
| HLJ1_G0048980.mRNA.1.CDS.1 | D, d | protein | 254 | Saccharomyces cerevisiae | A0A6A5Q273 |
| EM14S01-3B_G0035190.mRNA.1.CDS.1 | E, e | protein | 260 | Saccharomyces cerevisiae | A0A6A5PXN2 |
| BJ4_G0043800.mRNA.1.CDS.1 | F, f | protein | 234 | Saccharomyces cerevisiae | A0A6A5PTH4 |
| Probable proteasome subunit alpha type-7 | G, g | protein | 288 | Saccharomyces cerevisiae | A0A6A5Q4M4 |
| Proteasome subunit beta type-1 | 1, h | protein | 215 | Saccharomyces cerevisiae | P38624 |
| Proteasome endopeptidase complex | 2, i | protein | 261 | Saccharomyces cerevisiae | A0A6A5Q449 |
| Proteasome endopeptidase complex | 3, j | protein | 205 | Saccharomyces cerevisiae | A0A6L0YA22 |
| Proteasome subunit beta | 4, k | protein | 198 | Saccharomyces cerevisiae | A0A6A5Q0W2 |
| Proteasome subunit beta type-5 | 5, l | protein | 287 | Saccharomyces cerevisiae | A0A6A5Q5W3 |
23 more molecules are not listed.
Sequence of entity 1 (A, a), FASTA
>7QO6_1 BJ4_G0020160.mRNA.1.CDS.1 (chains A, a)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD
Sequence of entity 2 (B, b), FASTA
>7QO6_2 HLJ1_G0039880.mRNA.1.CDS.1 (chains B, b)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL
Sequence of entity 3 (C, c), FASTA
>7QO6_3 BJ4_G0021480.mRNA.1.CDS.1 (chains C, c)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK
Sequence of entity 4 (D, d), FASTA
>7QO6_4 HLJ1_G0048980.mRNA.1.CDS.1 (chains D, d)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH
Sequence of entity 5 (E, e), FASTA
>7QO6_5 EM14S01-3B_G0035190.mRNA.1.CDS.1 (chains E, e)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS
Sequence of entity 6 (F, f), FASTA
>7QO6_6 BJ4_G0043800.mRNA.1.CDS.1 (chains F, f)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI
Sequence of entity 7 (G, g), FASTA
>7QO6_7 Probable proteasome subunit alpha type-7 (chains G, g)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE
Sequence of entity 8 (1, h), FASTA
>7QO6_8 Proteasome subunit beta type-1 (chains 1, h)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL
Sequence of entity 9 (2, i), FASTA
>7QO6_9 Proteasome endopeptidase complex (chains 2, i)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA
Sequence of entity 10 (3, j), FASTA
>7QO6_10 Proteasome endopeptidase complex (chains 3, j)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD
Sequence of entity 11 (4, k), FASTA
>7QO6_11 Proteasome subunit beta (chains 4, k)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ
Sequence of entity 12 (5, l), FASTA
>7QO6_12 Proteasome subunit beta type-5 (chains 5, l)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 5 |
| MG | Magnesium ion | Mg | 6 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
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
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