8FTQ: HRpn13 Pru domain

Crystal structure of hRpn13 Pru domain in complex with Ubiquitin and XL44. Determined by X-ray diffraction at 2.1 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,175
Mol. weight: 50.39 kDa
Ligands: ZTO
Released: 27 Mar 2024

Explore 8FTQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FTQ contains 10 α-helices and 32 β-strands across 4 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 A and B: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	1
β-strand	28-34	7	2
β-strand	37-40	4	2
β-strand	45-51	7	1
β-strand	57-63	7	1
β-strand	69-75	7	1
β-strand	80-84	5	2
β-strand	93-98	6	2
β-strand	104-109	6	2
α-helix	117-129	13

Chains C and D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	5
β-strand	13-16	4	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-71	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proteasomal ubiquitin receptor ADRM1	A, B	protein	149	Homo sapiens	Q16186 (AlphaFold model)
Ubiquitin	C, D	protein	72	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8FTQ_1 Proteasomal ubiquitin receptor ADRM1 (chains A, B)
TTSGALFPSLVPGSRGASNKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCW
KDRTSGNVEDDLIIFPDDCEFKRVPQCPSGRVYVLKFKAGSKRLFFWMQEPKTDQDEEHC
RKVNEYLNNPPMPGALGASGSSGHELSAL

Sequence of entity 2 (C, D), FASTA

>8FTQ_2 Ubiquitin (chains C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLR

Ligands and cofactors

ID	Name	Formula	Copies
ZTO	N-(3-{[(3R)-5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}phenyl)-4-methoxybe…	C23 H19 F N2 O3	2

Primary citation

A structure-based designed small molecule depletes hRpn13 Pru and a select group of KEN box proteins. Lu, X., Chandravanshi, M., Sabbasani, V.R. et al. Nat Commun (2024) 15:2485-2485. DOI 10.1038/s41467-024-46644-7 · PubMed

Other PDB entries of the same protein (UniProt Q16186 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex
6OI4 1.76 Å, RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex
5IRS 1.8 Å, crystal structure of the proteasomal Rpn13 PRU-domain
8VWO 1.85 Å, Crystal structure of hRpn13 Pru bound with U-shaped peptide
4WLR 2.0 Å, Crystal Structure of mUCH37-hRPN13 CTD-hUb complex
5V1Z 2.0 Å, Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex
4UEL 2.3 Å, UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
9E7K 2.41 Å, Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in…
4UEM 2.82 Å, UCH-L5 in complex with the RPN13 DEUBAD domain
4WLQ 2.85 Å, Crystal structure of mUCH37-hRPN13 CTD complex
2KQZ Solution structure of the Rpn13 DEUBAD domain
2KR0 Solution structure of the proteasome ubiquitin receptor Rpn13

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