9UG9: 26S proteasome-Midnolin complex MB state
The cryo-EM structure of 26S proteasome-Midnolin complex MB state. Determined by electron microscopy at 3.5 Å resolution. Released 10 Sept 2025.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Homo sapiens
- Chains
- 48
- Atoms
- 103,692
- Mol. weight
- 1718.87 kDa
- Ligands
- ADP, ZN, ATP
- Released
- 10 Sept 2025
Explore 9UG9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9UG9 contains 572 α-helices and 558 β-strands across 48 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: 19 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| α-helix | 23-30 | 8 | |
| α-helix | 35-44 | 10 | |
| α-helix | 54-64 | 11 | |
| α-helix | 73-87 | 15 | |
| α-helix | 92-103 | 12 | |
| α-helix | 111-122 | 12 | |
| α-helix | 131-141 | 11 | |
| α-helix | 150-162 | 13 | |
| α-helix | 171-182 | 12 | |
| α-helix | 190-204 | 15 | |
| α-helix | 220-222 | 3 | |
| α-helix | 231-242 | 12 | |
| α-helix | 252-255 | 4 | |
| α-helix | 265-278 | 14 | |
| α-helix | 279-281 | 3 | |
| β-strand | 291-292 | 2 | 88 |
| α-helix | 293-299 | 7 | |
| α-helix | 307-317 | 11 | |
| β-strand | 320 | 1 | 89 |
| β-strand | 323-325 | 3 | 88 |
| β-strand | 330-332 | 3 | 88 |
| β-strand | 336 | 1 | 89 |
| α-helix | 343-369 | 27 | |
Chain A: 15 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 44-63 | 20 | |
| α-helix | 84-88 | 5 | |
| β-strand | 97-103 | 7 | 39 |
| β-strand | 111-114 | 4 | 39 |
| β-strand | 120-125 | 6 | 39 |
| β-strand | 139-142 | 4 | 39 |
| β-strand | 148-152 | 5 | 39 |
| α-helix | 154-156 | 3 | |
| α-helix | 159-162 | 4 | |
| β-strand | 165 | 1 | 113 |
| α-helix | 174-177 | 4 | |
| α-helix | 181-196 | 16 | |
| α-helix | 200-204 | 5 | |
| β-strand | 211-215 | 5 | 113 |
| α-helix | 222-231 | 10 | |
| β-strand | 236-240 | 5 | 113 |
| β-strand | 249 | 1 | 114 |
| α-helix | 252-266 | 15 | |
| β-strand | 270-274 | 5 | 113 |
| α-helix | 294-306 | 13 | |
| β-strand | 316-321 | 6 | 113 |
| α-helix | 329-332 | 4 | |
| β-strand | 339-342 | 4 | 113 |
| α-helix | 349-358 | 10 | |
| α-helix | 371-376 | 6 | |
| α-helix | 382-398 | 17 | |
| α-helix | 406-425 | 20 | |
Chain b: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-10 | 7 | 115 |
| α-helix | 25-41 | 17 | |
| β-strand | 48-53 | 6 | 115 |
| β-strand | 62-65 | 4 | 115 |
| α-helix | 69-74 | 6 | |
| α-helix | 87-96 | 10 | |
| β-strand | 106-113 | 8 | 115 |
| α-helix | 121-133 | 13 | |
| β-strand | 137-142 | 6 | 115 |
| α-helix | 154-160 | 7 | |
| β-strand | 171 | 1 | 115 |
| α-helix | 172-174 | 3 | |
| α-helix | 180-183 | 4 | |
| α-helix | 186-188 | 3 | |
Chain B: 21 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 59-85 | 27 | |
| α-helix | 91-95 | 5 | |
| α-helix | 96-102 | 7 | |
| β-strand | 107-111 | 5 | 39 |
| β-strand | 112-115 | 4 | 43 |
| β-strand | 120 | 1 | 44 |
| β-strand | 121-123 | 3 | 43 |
| α-helix | 133 | 1 | |
| β-strand | 134 | 1 | 44 |
| α-helix | 135 | 1 | |
| β-strand | 149-152 | 4 | 39 |
| β-strand | 159-162 | 4 | 39 |
| α-helix | 163-168 | 6 | |
| α-helix | 169-174 | 6 | |
| β-strand | 175 | 1 | 45 |
| α-helix | 192-197 | 6 | |
| α-helix | 198-202 | 5 | |
| α-helix | 203-206 | 4 | |
| α-helix | 217-219 | 3 | |
| β-strand | 221-225 | 5 | 45 |
| α-helix | 234-239 | 6 | |
| β-strand | 247-251 | 5 | 45 |
| α-helix | 262-277 | 16 | |
| β-strand | 281-285 | 5 | 45 |
| α-helix | 287-289 | 3 | |
| α-helix | 301-316 | 16 | |
| α-helix | 321-322 | 2 | |
| β-strand | 326-330 | 5 | 45 |
| α-helix | 339-342 | 4 | |
| β-strand | 349-352 | 4 | 45 |
| α-helix | 354-356 | 3 | |
| α-helix | 359-368 | 10 | |
| α-helix | 392-409 | 18 | |
| α-helix | 416-430 | 15 | |
Chain c: 9 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-33 | 4 | 132 |
| α-helix | 35-47 | 13 | |
| β-strand | 56-60 | 5 | 132 |
| β-strand | 66-73 | 8 | 132 |
| β-strand | 78-79 | 2 | 3 |
| β-strand | 83-85 | 3 | 3 |
| α-helix | 90-101 | 12 | |
| β-strand | 107-114 | 8 | 132 |
| α-helix | 126-136 | 11 | |
| β-strand | 141-145 | 5 | 132 |
| β-strand | 151 | 1 | 133 |
| β-strand | 154 | 1 | 133 |
| β-strand | 157-162 | 6 | 132 |
| α-helix | 191-194 | 4 | |
| β-strand | 200-203 | 4 | 132 |
| β-strand | 205-207 | 3 | 132 |
| α-helix | 211-217 | 7 | |
| α-helix | 225-228 | 4 | |
| α-helix | 234-261 | 28 | |
| α-helix | 267-270 | 4 | |
| α-helix | 284-308 | 25 | |
Chain C: 21 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-65 | 45 | |
| β-strand | 72-79 | 8 | 39 |
| β-strand | 84-88 | 5 | 39 |
| β-strand | 94-98 | 5 | 39 |
| β-strand | 113-116 | 4 | 39 |
| β-strand | 122-126 | 5 | 39 |
| α-helix | 127-129 | 3 | |
| α-helix | 133-136 | 4 | |
| β-strand | 141-142 | 2 | 90 |
| α-helix | 155-161 | 7 | |
| α-helix | 162-166 | 5 | |
| α-helix | 167-170 | 4 | |
| α-helix | 172-178 | 7 | |
| α-helix | 180-183 | 4 | |
| β-strand | 185-188 | 4 | 90 |
| α-helix | 198-206 | 9 | |
| β-strand | 210-214 | 5 | 90 |
| α-helix | 221-223 | 3 | |
| α-helix | 226-240 | 15 | |
| β-strand | 244-248 | 5 | 90 |
| α-helix | 251-255 | 5 | |
| α-helix | 259-261 | 3 | |
| α-helix | 266-268 | 3 | |
| α-helix | 270-281 | 12 | |
| β-strand | 289-294 | 6 | 90 |
| α-helix | 303-306 | 4 | |
| β-strand | 314-315 | 2 | 90 |
| α-helix | 318-320 | 3 | |
| α-helix | 322-332 | 11 | |
| α-helix | 344-350 | 7 | |
| α-helix | 357-372 | 16 | |
| α-helix | 380-392 | 13 | |
Chain d: 15 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 112-123 | 12 | |
| α-helix | 135-157 | 23 | |
| α-helix | 162-175 | 14 | |
| α-helix | 182-185 | 4 | |
| α-helix | 192-201 | 10 | |
| α-helix | 206-211 | 6 | |
| α-helix | 218-220 | 3 | |
| α-helix | 227-236 | 10 | |
| α-helix | 241-246 | 6 | |
| α-helix | 247-249 | 3 | |
| α-helix | 258-274 | 17 | |
| β-strand | 282 | 1 | 6 |
| α-helix | 284-287 | 4 | |
| α-helix | 288-292 | 5 | |
| α-helix | 299-303 | 5 | |
| β-strand | 309 | 1 | 7 |
| β-strand | 315 | 1 | 6 |
| β-strand | 316 | 1 | 7 |
| α-helix | 332-347 | 16 | |
Chain D: 15 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-78 | 39 | |
| α-helix | 79-81 | 3 | |
| β-strand | 87-97 | 11 | 39 |
| β-strand | 100-105 | 6 | 39 |
| β-strand | 110-115 | 6 | 39 |
| β-strand | 129-132 | 4 | 39 |
| β-strand | 139-142 | 4 | 39 |
| α-helix | 171-179 | 9 | |
| α-helix | 183-185 | 3 | |
| α-helix | 189-192 | 4 | |
| β-strand | 201-205 | 5 | 67 |
| α-helix | 212-221 | 10 | |
| β-strand | 227-230 | 4 | 67 |
| α-helix | 242-257 | 16 | |
| β-strand | 261-265 | 5 | 67 |
| α-helix | 267-269 | 3 | |
| α-helix | 282-295 | 14 | |
| β-strand | 306-310 | 5 | 67 |
| α-helix | 319-322 | 4 | |
| β-strand | 329-332 | 4 | 67 |
| α-helix | 338-348 | 11 | |
| α-helix | 362-365 | 4 | |
| α-helix | 372-388 | 17 | |
| β-strand | 391 | 1 | 68 |
| α-helix | 396-406 | 11 | |
| α-helix | 415-417 | 3 | |
40 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 |
|---|
| Midnolin | u | protein | 491 | Homo sapiens | Q504T8 (AlphaFold model) |
| 26S proteasome non-ATPase regulatory subunit 8 | d | protein | 350 | Homo sapiens | P48556 (AlphaFold model) |
| Proteasome subunit alpha type-3 | M, m | protein | 255 | Homo sapiens | P25788 (AlphaFold model) |
| Proteasome subunit beta type-5 | R, r | protein | 263 | Homo sapiens | P28074 (AlphaFold model) |
| Proteasome subunit beta type-6 | N, n | protein | 239 | Homo sapiens | P28072 |
| 26S proteasome regulatory subunit 10B | E | protein | 389 | Homo sapiens | P62333 |
| 26S proteasome regulatory subunit 4 | B | protein | 440 | Homo sapiens | P62191 |
| 26S proteasome complex subunit SEM1 | e | protein | 70 | Homo sapiens | P60896 |
| Proteasome subunit beta type-7 | O, o | protein | 277 | Homo sapiens | Q99436 |
| Proteasome subunit beta type-1 | S, s | protein | 241 | Homo sapiens | P20618 |
| 26S proteasome regulatory subunit 6B | D | protein | 418 | Homo sapiens | P43686 |
| 26S proteasome regulatory subunit 6A | F | protein | 439 | Homo sapiens | P17980 |
22 more molecules are not listed.
Sequence of entity 1 (u), FASTA
>9UG9_1 Midnolin (chains u)
MMEPQPGGARSCRRGAPGGACELGPAAEAAPMSLAIHSTTGTRYDLAVPPDETVEGLRKR
LSQRLKVPKERLALLHKDTRLSSGKLQEFGVGDGSKLTLVPTVEAGLMSQASRPEQSVMQ
ALESLTETQVSDFLSGRSPLTLALRVGDHMMFVQLQLAAQHAPLQHRHVLAAAAAAAAAR
GDPSIASPVSSPCRPVSSAARVPPVPTSPSPASPSPITAGSFRSHAASTTCPEQMDCSPT
ASSSASPGASTTSTPGASPAPRSRKPGAVIESFVNHAPGVFSGTFSGTLHPNCQDSSGRP
RRDIGTILQILNDLLSATRHYQGMPPSLAQLRCHAQCSPASPAPDLAPRTTSCEKLTAAP
SASLLQGQSQIRMCKPPGDRLRQTENRATRCKVERLQLLLQQKRLRRKARRDARGPYHWS
PSRKAGRSDSSSSGGGGSPSEASGLGLDFEDSVWKPEVNPDIKSEFVVAGSDYKDDDDKG
SHHHHHHHHHH
Sequence of entity 2 (d), FASTA
>9UG9_2 26S proteasome non-ATPase regulatory subunit 8 (chains d)
MFIKGRAPRAPPRERRRATRGGLRQVVAPPRALGSTSRPHFRRASVCRRRCRKSGGLLAA
SRKMAAAAVNGAAGFSSSGPAATSGAVLQAATGMYEQLKGEWNRKSPNLSKCGEELGRLK
LVLLELNFLPTTGTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKE
QLPESAYMHQLLGLNLLFLLSQNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGS
YNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMT
DYAKKRGWVLGPNNYYSFASQQQKPEDTTIPSTELAKQVIEYARQLEMIV
Sequence of entity 3 (M, m), FASTA
>9UG9_3 Proteasome subunit alpha type-3 (chains M, m)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM
Sequence of entity 4 (R, r), FASTA
>9UG9_4 Proteasome subunit beta type-5 (chains R, r)
MALASVLERPLPVNQRGFFGLGGRADLLDLGPGSLSDGLSLAAPGWGVPEEPGIEMLHGT
TTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLAR
QCRIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRI
SGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVRE
DGWIRVSSDNVADLHEKYSGSTP
Sequence of entity 5 (N, n), FASTA
>9UG9_5 Proteasome subunit beta type-6 (chains N, n)
MAATLLAARGAGPAPAWGPEAFTPDWESREVSTGTTIMAVQFDGGVVLGADSRTTTGSYI
ANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEM
CYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREG
MTKEECLQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKFAVATLPPA
Sequence of entity 6 (E), FASTA
>9UG9_6 26S proteasome regulatory subunit 10B (chains E)
MADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEV
LKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVY
NMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGK
TLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYARDHQPCIIFMDEIDAIGG
RRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLDPALLRPGRLDRKIH
IDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVCTEAGMFAIRADHD
FVVQEDFMKAVRKVADSKKLESKLDYKPV
Sequence of entity 7 (B), FASTA
>9UG9_7 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL
Sequence of entity 8 (e), FASTA
>9UG9_8 26S proteasome complex subunit SEM1 (chains e)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS
Sequence of entity 9 (O, o), FASTA
>9UG9_9 Proteasome subunit beta type-7 (chains O, o)
MAAVSVYAPPVGGFSFDNCRRNAVLEADFAKRGYKLPKVRKTGTTIAGVVYKDGIVLGAD
TRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVV
TANRMLKQMLFRYQGYIGAALVLGGVDVTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAV
FEDKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISKNKLDFLRPYTVPNKKGT
RLGRYRCEKGTTAVLTEKITPLEIEVLEETVQTMDTS
Sequence of entity 10 (S, s), FASTA
>9UG9_10 Proteasome subunit beta type-1 (chains S, s)
MLSSTAMYSAPGRDLGMEPHRAAGPLQLRFSPYVFNGGTILAIAGEDFAIVASDTRLSEG
FSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAML
STILYSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQ
VGFKNMQNVEHVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGIREETVSLRK
D
Sequence of entity 11 (D), FASTA
>9UG9_11 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK
Sequence of entity 12 (F), FASTA
>9UG9_12 26S proteasome regulatory subunit 6A (chains F)
MNLLPNIESPVTRQEKMATVWDEAEQDGIGEEVLKMSTEEIIQRTRLLDSEIKIMKSEVL
RVTHELQAMKDKIKENSEKIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGK
CAVIKTSTRQTYFLPVIGLVDAEKLKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDER
PTEQYSDIGGLDKQIQELVEAIVLPMNHKEKFENLGIQPPKGVLMYGPPGTGKTLLARAC
AAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPSIIFIDELDAIGTKRFDSEK
AGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSGRLDRKIEFPMPNEE
ARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKAVCVEAGMIALRRGATELTHEDY
MEGILEVQAKKKANLQYYA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 2 |
| ZN | Zinc ion | Zn | 1 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 3 |
Primary citation
Structure-based engineering of the midnolin-proteasome pathway for targeted protein degradation. Wang, H., Zheng, Y., Wang, T. et al. Protein Cell (2026) 17:83-88. DOI 10.1093/procel/pwaf069 · PubMed
Other PDB entries of the same protein (UniProt Q504T8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9VEH 2.0 Å, The MIDN Catch-IRF4 (A8M) fusion protein
- 9VE3 2.1 Å, The MIDN Catch-IRF4 (V2L) fusion protein
- 9VE7 2.15 Å, The MIDN Catch-IRF4 (A8V) fusion protein
- 8VQP 2.52 Å, Crystal Structure Analysis of EGR1-MIDN
- 9VE4 2.55 Å, The MIDN Catch-IRF4 fusion protein
- 9MBP 2.75 Å, Substrate-engaged human 26S proteasome bound to midnolin with RPT1 at top of spiral…
- 9NKG 2.8 Å, Structure of substrate engaged MIDN-bound human 26S proteasome, EB-MIDN (Composite map)
- 9VE6 2.8 Å, The MIDN Catch-IRF4 (F6Y) fusion protein
- 9MBO 2.83 Å, Focused refinement of RPN1 and the C-terminal helix of midnolin in the substrate-engaged…
- 9VE8 2.85 Å, The MIDN Catch-IRF4 (A8L) fusion protein
- 9BV3 2.9 Å, M1B Midnolin-Proteasome
- 9NKI 2.94 Å, Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state…
Browse structure collections
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