9E7K: UCH37 RPN13 DEUBAD complex

Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in the canonical ubiquitin binding site. Determined by X-ray diffraction at 2.41 Å resolution. Released 3 Sept 2025.

Method: X-ray diffraction
Resolution: 2.41 Å
Organisms: Homo sapiens, Camelidae mixed library
Chains: 3
Atoms: 3,769
Mol. weight: 65.59 kDa
Released: 3 Sept 2025

Explore 9E7K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E7K contains 22 α-helices and 21 β-strands across 3 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: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	15-24	10
β-strand	28	1	1
β-strand	30-34	5	2
α-helix	40-43	4
β-strand	49-56	8	2
α-helix	85-87	3
α-helix	88-97	10
β-strand	106	1	1
α-helix	109-117	9
α-helix	123-131	9
α-helix	134-142	9
β-strand	164-171	8	2
β-strand	174-179	6	2
β-strand	186-190	5	2
α-helix	196-213	18
β-strand	218-225	8	2
α-helix	227-244	18
α-helix	256-288	33
α-helix	292-305	14

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	288-290	3
α-helix	298-301	4
α-helix	304-308	5
α-helix	324-331	8
α-helix	334-347	14
α-helix	363-371	9
α-helix	374-383	10

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	3
β-strand	28	1	4
β-strand	31-33	3	5
β-strand	38-44	7	4
β-strand	45-46	2	3
β-strand	54-60	7	5
β-strand	67-73	7	5
β-strand	77-80	4	5
α-helix	82-84	3
β-strand	88-93	6	4
β-strand	98-104	7	4
α-helix	108-110	3
β-strand	112-119	8	5
α-helix	122-124	3
β-strand	126-127	2	5
β-strand	131-135	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5	A	protein	328	Homo sapiens	Q9Y5K5 (AlphaFold model)
Nb-cS1	C	protein	137	Camelidae mixed library
Proteasomal ubiquitin receptor ADRM1	B	protein	126	Homo sapiens	Q16186 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9E7K_1 Isoform 3 of Ubiquitin carboxyl-terminal hydrolase isozyme L5 (chains A)
MTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQP
GEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQS
FDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDG
LREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQR
QLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLK
TLAEHQQLIPLVEKAKEKQNAKKAQETK

Sequence of entity 2 (C), FASTA

>9E7K_2 Nb-cS1 (chains C)
MGSSHHHHHHSSGLVPRGSHMQVQLQESGGGLVQAGGSLRLSCAASGYISRPRTMGWYRQ
APGKEREFVAIISNGAITNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAGR
NIWHAYWGQGTQVTVSS

Sequence of entity 3 (B), FASTA

>9E7K_3 Proteasomal ubiquitin receptor ADRM1 (chains B)
GPLGSMSILATMNVPAGPAGGQQVDLASVLTPEIMAPILANADVQERLLPYLPSGESLPQ
TADEIQNTLTSPQFQQALGMFSAALASGQLGPLMCQFGLPAEAVEAANKGDVEAFAKAMQ
NNAKPE

Primary citation

Site-Specific Nanobody Inhibitors of the Proteasomal Deubiquitinase UCH37. Li, Y., Chang, L.H., Patel, R. et al. bioRxiv (2025). DOI 10.1101/2025.08.11.669711 · PubMed

Other PDB entries of the same protein (UniProt Q9Y5K5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3RII 2.0 Å, Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human…
3A7S 2.2 Å, Catalytic domain of UCH37
3TB3 2.3 Å, Crystal structure of the UCH domain of UCH-L5 with 6 residues deleted
4UEL 2.3 Å, UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
3RIS 2.4 Å, Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human…
4UEM 2.82 Å, UCH-L5 in complex with the RPN13 DEUBAD domain
3IHR 2.95 Å, Crystal Structure of Uch37
4WLP 3.1 Å, Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating Complex
4UF6 3.69 Å, UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G
4UF5 3.7 Å, Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G

Browse structure collections

About this viewer

MolViewer shows 9E7K directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.