6EF2: Yeast 26S proteasome
Yeast 26S proteasome bound to ubiquitinated substrate (5T motor state). Determined by electron microscopy at 4.27 Å resolution. Released 17 Oct 2018.
- Method
- Electron microscopy
- Resolution
- 4.27 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
- Chains
- 14
- Atoms
- 24,659
- Mol. weight
- 368.2 kDa
- Ligands
- ATP, ADP
- Released
- 17 Oct 2018
Explore 6EF2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6EF2 contains 148 α-helices and 140 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: 8 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-33 | 7 | |
| β-strand | 42-46 | 5 | 1 |
| β-strand | 51-56 | 6 | 1 |
| β-strand | 64 | 1 | 2 |
| β-strand | 72 | 1 | 3 |
| β-strand | 79-82 | 4 | 3 |
| α-helix | 87-108 | 22 | |
| α-helix | 111-113 | 3 | |
| α-helix | 114-127 | 14 | |
| α-helix | 135-137 | 3 | |
| β-strand | 142-146 | 5 | 3 |
| β-strand | 152-156 | 5 | 3 |
| β-strand | 164 | 1 | 3 |
| β-strand | 166 | 1 | 4 |
| β-strand | 170 | 1 | 1 |
| α-helix | 175-187 | 13 | |
| α-helix | 199-214 | 16 | |
| β-strand | 223-229 | 7 | 1 |
| β-strand | 232-236 | 5 | 1 |
| α-helix | 243-246 | 4 | |
Chain B: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-30 | 10 | |
| β-strand | 34-38 | 5 | 5 |
| β-strand | 43-48 | 6 | 5 |
| β-strand | 56 | 1 | 4 |
| β-strand | 65-66 | 2 | 6 |
| β-strand | 72-75 | 4 | 6 |
| α-helix | 85-92 | 8 | |
| α-helix | 93-98 | 6 | |
| α-helix | 99-101 | 3 | |
| α-helix | 108-118 | 11 | |
| β-strand | 134-138 | 5 | 6 |
| β-strand | 146-150 | 5 | 6 |
| β-strand | 156-159 | 4 | 6 |
| β-strand | 161-164 | 4 | 5 |
| α-helix | 169-177 | 9 | |
| α-helix | 186-196 | 11 | |
| β-strand | 209-214 | 6 | 5 |
| α-helix | 219-221 | 3 | |
| β-strand | 235-237 | 3 | 5 |
| α-helix | 240-244 | 5 | |
| α-helix | 246-248 | 3 | |
Chain C: 9 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-26 | 7 | |
| α-helix | 28-31 | 4 | |
| β-strand | 35-38 | 4 | 7 |
| β-strand | 45-46 | 2 | 7 |
| β-strand | 68 | 1 | 8 |
| β-strand | 74-76 | 3 | 8 |
| β-strand | 80 | 1 | 9 |
| α-helix | 82-102 | 21 | |
| α-helix | 108-116 | 9 | |
| β-strand | 136-141 | 6 | 8 |
| β-strand | 145-150 | 6 | 8 |
| β-strand | 158-159 | 2 | 8 |
| β-strand | 160 | 1 | 10 |
| β-strand | 162-165 | 4 | 7 |
| α-helix | 169-177 | 9 | |
| α-helix | 187-199 | 13 | |
| α-helix | 208-210 | 3 | |
| β-strand | 214-215 | 2 | 7 |
| β-strand | 216-217 | 2 | 11 |
| β-strand | 226-227 | 2 | 11 |
| α-helix | 232-234 | 3 | |
| α-helix | 236-240 | 5 | |
Chain D: 9 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-27 | 5 | |
| β-strand | 35-37 | 3 | 12 |
| β-strand | 42-44 | 3 | 12 |
| β-strand | 55 | 1 | 10 |
| β-strand | 68 | 1 | 13 |
| β-strand | 71-77 | 7 | 13 |
| α-helix | 80-100 | 21 | |
| α-helix | 106-117 | 12 | |
| α-helix | 119-122 | 4 | |
| β-strand | 131-138 | 8 | 13 |
| β-strand | 145-151 | 7 | 13 |
| β-strand | 155-157 | 3 | 13 |
| β-strand | 159 | 1 | 14 |
| β-strand | 161-162 | 2 | 12 |
| α-helix | 168-178 | 11 | |
| α-helix | 188-195 | 8 | |
| α-helix | 200-203 | 4 | |
| β-strand | 213-215 | 3 | 12 |
| β-strand | 221-222 | 2 | 12 |
| α-helix | 227-230 | 4 | |
| α-helix | 232-238 | 7 | |
Chain E: 11 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-31 | 9 | |
| β-strand | 38-41 | 4 | 15 |
| β-strand | 46-49 | 4 | 15 |
| β-strand | 50 | 1 | 16 |
| β-strand | 59 | 1 | 14 |
| α-helix | 61-63 | 3 | |
| β-strand | 74-75 | 2 | 17 |
| β-strand | 80 | 1 | 18 |
| α-helix | 82-92 | 11 | |
| α-helix | 95-102 | 8 | |
| α-helix | 109-120 | 12 | |
| α-helix | 121-123 | 3 | |
| β-strand | 140 | 1 | 18 |
| β-strand | 142 | 1 | 19 |
| β-strand | 145-148 | 4 | 17 |
| β-strand | 152-154 | 3 | 17 |
| β-strand | 157-158 | 2 | 19 |
| β-strand | 164-165 | 2 | 19 |
| β-strand | 169-171 | 3 | 15 |
| α-helix | 179-182 | 4 | |
| α-helix | 183-185 | 3 | |
| α-helix | 197-206 | 10 | |
| α-helix | 211-212 | 2 | |
| β-strand | 218 | 1 | 16 |
| β-strand | 220-223 | 4 | 15 |
| β-strand | 227-230 | 4 | 15 |
| α-helix | 233-247 | 15 | |
Chain F: 9 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-25 | 6 | |
| α-helix | 29-31 | 3 | |
| β-strand | 35-38 | 4 | 20 |
| β-strand | 43-48 | 6 | 20 |
| β-strand | 63-67 | 5 | 21 |
| β-strand | 70-76 | 7 | 21 |
| α-helix | 79-91 | 13 | |
| α-helix | 101-104 | 4 | |
| α-helix | 105-121 | 17 | |
| β-strand | 130-136 | 7 | 21 |
| β-strand | 143-147 | 5 | 21 |
| β-strand | 155 | 1 | 21 |
| β-strand | 156 | 1 | 22 |
| β-strand | 159-161 | 3 | 20 |
| α-helix | 166-175 | 10 | |
| α-helix | 186-197 | 12 | |
| α-helix | 208-210 | 3 | |
| β-strand | 212-217 | 6 | 20 |
| β-strand | 220-225 | 6 | 20 |
| α-helix | 227-229 | 3 | |
Chain G: 11 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-31 | 10 | |
| β-strand | 38-40 | 3 | 23 |
| β-strand | 41 | 1 | 24 |
| β-strand | 46-48 | 3 | 24 |
| β-strand | 51-53 | 3 | 25 |
| β-strand | 59 | 1 | 22 |
| α-helix | 60 | 1 | |
| β-strand | 67-70 | 4 | 26 |
| β-strand | 74-80 | 7 | 26 |
| α-helix | 84-96 | 13 | |
| α-helix | 100-103 | 4 | |
| α-helix | 109-122 | 14 | |
| β-strand | 134-140 | 7 | 26 |
| β-strand | 141-142 | 2 | 27 |
| β-strand | 145-146 | 2 | 27 |
| β-strand | 149-150 | 2 | 26 |
| β-strand | 158 | 1 | 26 |
| β-strand | 160 | 1 | 2 |
| β-strand | 162-164 | 3 | 23 |
| α-helix | 169-175 | 7 | |
| α-helix | 177-182 | 6 | |
| α-helix | 190-204 | 15 | |
| α-helix | 205-207 | 3 | |
| β-strand | 212-214 | 3 | 25 |
| β-strand | 217-220 | 4 | 24 |
| β-strand | 227-229 | 3 | 24 |
| α-helix | 236-239 | 4 | |
| α-helix | 241-247 | 7 | |
Chain H: 14 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 195-198 | 4 | |
| β-strand | 200 | 1 | 28 |
| α-helix | 217-224 | 8 | |
| α-helix | 226-230 | 5 | |
| α-helix | 232-238 | 7 | |
| α-helix | 241-243 | 3 | |
| β-strand | 246 | 1 | 29 |
| β-strand | 247-249 | 3 | 30 |
| α-helix | 257-267 | 11 | |
| β-strand | 270-274 | 5 | 28 |
| α-helix | 288-300 | 13 | |
| β-strand | 304-308 | 5 | 28 |
| α-helix | 328-340 | 13 | |
| β-strand | 349-350 | 2 | 28 |
| β-strand | 352 | 1 | 29 |
| β-strand | 355 | 1 | 30 |
| α-helix | 358-360 | 3 | |
| β-strand | 374-376 | 3 | 30 |
| α-helix | 382-385 | 4 | |
| α-helix | 389-392 | 4 | |
| β-strand | 398 | 1 | 31 |
| α-helix | 404-410 | 7 | |
| α-helix | 418-432 | 15 | |
| β-strand | 438 | 1 | 31 |
| α-helix | 441-451 | 11 | |
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 | 249 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P23639 (AlphaFold model) |
| Proteasome subunit alpha type-3 | C | protein | 241 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P23638 (AlphaFold model) |
| Proteasome subunit alpha type-4 | D | protein | 241 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40303 (AlphaFold model) |
| Proteasome subunit alpha type-5 | E | protein | 247 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32379 |
| Proteasome subunit alpha type-6 | F | protein | 232 | 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 | 273 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33299 |
| 26S proteasome regulatory subunit 4 homolog | I | protein | 260 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40327 |
| 26S proteasome regulatory subunit 8 homolog | J | protein | 262 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q01939 |
| 26S proteasome regulatory subunit 6B homolog | K | protein | 259 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33298 |
| 26S proteasome subunit RPT4 | L | protein | 264 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P53549 |
2 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6EF2_1 Proteasome subunit alpha type-1 (chains A)
AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTV
SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYT
QRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKS
KIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVA
Sequence of entity 2 (B), FASTA
>6EF2_2 Proteasome subunit alpha type-2 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEA
Sequence of entity 3 (C), FASTA
>6EF2_3 Proteasome subunit alpha type-3 (chains C)
RRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTST
EKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYT
QHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDD
MKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTG
I
Sequence of entity 4 (D), FASTA
>6EF2_4 Proteasome subunit alpha type-4 (chains D)
SGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITP
SKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYT
QSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDR
KEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQ
E
Sequence of entity 5 (E), FASTA
>6EF2_5 Proteasome subunit alpha type-5 (chains E)
FLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLES
DSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLAL
RFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQA
ELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIK
ELKEKEA
Sequence of entity 6 (F), FASTA
>6EF2_6 Proteasome subunit alpha type-6 (chains F)
RNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKK
IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS
YGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKI
DGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI
Sequence of entity 7 (G), FASTA
>6EF2_7 Probable proteasome subunit alpha type-7 (chains G)
SIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQ
KNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQA
HTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDH
HPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDF
AQKEIN
Sequence of entity 8 (H), FASTA
>6EF2_8 26S proteasome regulatory subunit 7 homolog (chains H)
SVTMMTVEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPG
TGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDA
VGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDR
KVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRA
RRKVATEKDFLKAVDKVISGYKKFSSTSRYMQY
Sequence of entity 9 (I), FASTA
>6EF2_9 26S proteasome regulatory subunit 4 homolog (chains I)
TESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVA
NQTSATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLST
KKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTEAGLLALRERRMQVTAEDFK
QAKERVMKNKVEENLEGLYL
Sequence of entity 10 (J), FASTA
>6EF2_10 26S proteasome regulatory subunit 8 homolog (chains J)
DSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVA
HHTDCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGG
GDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAA
RAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTEAGMYALRERRIHVTQEDFE
LAVGKVMNKNQETAISVAKLFK
Sequence of entity 11 (K), FASTA
>6EF2_11 26S proteasome regulatory subunit 6B homolog (chains K)
TYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANS
TKAAFIRVNGSEFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSD
REVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRER
RLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDLEE
AYATQVKTDNTVDKFDFYK
Sequence of entity 12 (L), FASTA
>6EF2_12 26S proteasome subunit RPT4 (chains L)
LVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPG
TGKTLLAKAVAATIGANFIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEVDA
IGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDR
KVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATEAGFFAIRD
DRDHINPDDLMKAVRKVAEVKKLE
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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