9MBO: Midnolin

Focused refinement of RPN1 and the C-terminal helix of midnolin in the substrate-engaged human 26S proteasome. Determined by electron microscopy at 2.83 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 2.83 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,770
Mol. weight: 149.59 kDa
Released: 25 Mar 2026

Explore 9MBO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MBO contains 52 α-helices and 13 β-strands across 2 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	378-411	34

Chain B: 51 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	47-63	17
α-helix	71-87	17
α-helix	100-102	3
α-helix	103-112	10
α-helix	114	1
α-helix	117-130	14
α-helix	141-144	4
α-helix	151-154	4
α-helix	156-172	17
α-helix	181-197	17
α-helix	201-210	10
α-helix	214-216	3
α-helix	226-235	10
α-helix	244-258	15
α-helix	262-272	11
α-helix	275-283	9
α-helix	288-301	14
α-helix	314-321	8
α-helix	326-337	12
α-helix	346-349	4
α-helix	351-353	3
α-helix	368-381	14
α-helix	395-399	5
α-helix	405-411	7
α-helix	413-417	5
α-helix	422-428	7
α-helix	438-451	14
α-helix	475-488	14
α-helix	495-501	7
α-helix	502-504	3
α-helix	512-525	14
α-helix	532-543	12
α-helix	553-556	4
α-helix	557-565	9
α-helix	571-573	3
α-helix	574-579	6
α-helix	585-599	15
α-helix	606-616	11
α-helix	650-660	11
α-helix	665-680	16
α-helix	684-687	4
α-helix	690-697	8
α-helix	704-713	10
α-helix	719-732	14
α-helix	739-751	13
α-helix	756-769	14
α-helix	771-774	4
β-strand	776-777	2	1
β-strand	781-782	2	2
β-strand	787-788	2	2
α-helix	790-802	13
α-helix	803-805	3
α-helix	806-813	8
α-helix	815-824	10
β-strand	826-827	2	1
β-strand	830-833	4	3
β-strand	839	1	3
β-strand	843-850	8	4
β-strand	861-869	9	4
β-strand	872	1	3
β-strand	878-882	5	4
β-strand	887-889	3	5
β-strand	896-899	4	3
β-strand	900-902	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Midnolin	A	protein	468	Homo sapiens	Q504T8 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 2	B	protein	908	Homo sapiens	Q13200 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9MBO_1 Midnolin (chains A)
MEPQPGGARSCRRGAPGGACELGPAAEAAPMSLAIHSTTGTRYDLAVPPDETVEGLRKRL
SQRLKVPKERLALLHKDTRLSSGKLQEFGVGDGSKLTLVPTVEAGLMSQASRPEQSVMQA
LESLTETQVSDFLSGRSPLTLALRVGDHMMFVQLQLAAQHAPLQHRHVLAAAAAAAAARG
DPSIASPVSSPCRPVSSAARVPPVPTSPSPASPSPITAGSFRSHAASTTCPEQMDCSPTA
SSSASPGASTTSTPGASPAPRSRKPGAVIESFVNHAPGVFSGTFSGTLHPNCQDSSGRPR
RDIGTILQILNDLLSATRHYQGMPPSLAQLRCHAQCSPASPAPDLAPRTTSCEKLTAAPS
ASLLQGQSQIRMCKPPGDRLRQTENRATRCKVERLQLLLQQKRLRRKARRDARGPYHWSP
SRKAGRSDSSSSGGGGSPSEASGLGLDFEDSVWKPEVNPDIKSEFVVA

Sequence of entity 2 (B), FASTA

>9MBO_2 26S proteasome non-ATPase regulatory subunit 2 (chains B)
MEEGGRDKAPVQPQQSPAAAPGGTDEKPSGKERRDAGDKDKEQELSEEDKQLQDELEMLV
ERLGEKDTSLYRPALEELRRQIRSSTTSMTSVPKPLKFLRPHYGKLKEIYENMAPGENKR
FAADIISVLAMTMSGERECLKYRLVGSQEELASWGHEYVRHLAGEVAKEWQELDDAEKVQ
REPLLTLVKEIVPYNMAHNAEHEACDLLMEIEQVDMLEKDIDENAYAKVCLYLTSCVNYV
PEPENSALLRCALGVFRKFSRFPEALRLALMLNDMELVEDIFTSCKDVVVQKQMAFMLGR
HGVFLELSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPKVPDDIYKTHLENNRFGG
SGSQVDSARMNLASSFVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILLW
DVDGGLTQIDKYLYSSEDYIKSGALLACGIVNSGVRNECDPALALLSDYVLHNSNTMRLG
SIFGLGLAYAGSNREDVLTLLLPVMGDSKSSMEVAGVTALACGMIAVGSCNGDVTSTILQ
TIMEKSETELKDTYARWLPLGLGLNHLGKGEAIEAILAALEVVSEPFRSFANTLVDVCAY
AGSGNVLKVQQLLHICSEHFDSKEKEEDKDKKEKKDKDKKEAPADMGAHQGVAVLGIALI
AMGEEIGAEMALRTFGHLLRYGEPTLRRAVPLALALISVSNPRLNILDTLSKFSHDADPE
VSYNSIFAMGMVGSGTNNARLAAMLRQLAQYHAKDPNNLFMVRLAQGLTHLGKGTLTLCP
YHSDRQLMSQVAVAGLLTVLVSFLDVRNIILGKSHYVLYGLVAAMQPRMLVTFDEELRPL
PVSVRVGQAVDVVGQAGKPKTITGFQTHTTPVLLAHGERAELATEEFLPVTPILEGFVIL
RKNPNYDL

Primary citation

Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover. Zhu, C., Qin, L., Dai, Z. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-71002-0 · 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
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…
21IK 2.99 Å, The MIDN Catch-IRF4 (V2T) fusion protein

Browse structure collections

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