2NBV: Rpn13 Pru domain engaging the hPLIC2 UBL domain

Solution structure of the Rpn13 Pru domain engaging the hPLIC2 UBL domain. Determined by solution NMR. Released 20 Jul 2016.

Method: Solution NMR
Organism: Homo sapiens
Chains: 2
Atoms: 1,529
Mol. weight: 25.51 kDa
Released: 20 Jul 2016

Explore 2NBV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NBV contains 5 α-helices and 16 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: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	1
β-strand	28-30	3	2
β-strand	31-34	4	3
β-strand	37-40	4	3
α-helix	41	1
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	114-116	3
α-helix	117-129	13

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	32-38	7	4
β-strand	43-49	7	4
α-helix	54-64	11
β-strand	73-75	3	4
β-strand	78	1	1
β-strand	80-81	2	4
α-helix	87-91	5
β-strand	96-101	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proteasomal ubiquitin receptor ADRM1	A	protein	150	Homo sapiens	Q16186 (AlphaFold model)
Ubiquilin-2	B	protein	78	Homo sapiens	Q9UHD9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2NBV_1 Proteasomal ubiquitin receptor ADRM1 (chains A)
MTTSGALFPSLVPGSRGASNKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFC
WKDRTSGNVEDDLIIFPDDCEFKRVPQCPSGRVYVLKFKAGSKRLFFWMQEPKTDQDEEH
CRKVNEYLNNPPMPGALGASGSSGHELSAL

Sequence of entity 2 (B), FASTA

>2NBV_2 Ubiquilin-2 (chains B)
APAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQD
TLIQHGIHDGLTVHLVIK

Primary citation

Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome. Chen, X., Randles, L., Shi, K. et al. Structure (2016) 24:1257-1270. DOI 10.1016/j.str.2016.05.018 · 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
8FTQ 2.1 Å, Crystal structure of hRpn13 Pru domain in complex with Ubiquitin and XL44
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

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