5V1Z: RPN13 PRU-RPN2 (932-953)-ubiquitin complex

Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 3 May 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,319
Mol. weight: 49.35 kDa
Released: 3 May 2017

Explore 5V1Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V1Z contains 12 α-helices and 35 β-strands across 6 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: 2 helices, 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	69-74	6	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: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	3
β-strand	28-30	3	4
β-strand	31-34	4	5
β-strand	37-40	4	5
β-strand	45-51	7	3
β-strand	57-63	7	3
β-strand	69-74	6	3
β-strand	80-85	6	4
β-strand	93-98	6	4
β-strand	104-109	6	4
α-helix	117-129	13

Chain C: 3 helices, 7 β-strands

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

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	8
β-strand	48-49	2	8
α-helix	50-51	2
β-strand	55	1	9
α-helix	57-59	3
β-strand	66-71	6	8

Chain E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	942-946	5
β-strand	948-949	2	2

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	941-947	7
β-strand	948-949	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proteasomal ubiquitin receptor ADRM1	A, B	protein	115	Homo sapiens	Q16186 (AlphaFold model)
Ubiquitin	C, D	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 1	E, F	protein	22	Homo sapiens	Q99460 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5V1Z_1 Proteasomal ubiquitin receptor ADRM1 (chains A, B)
PSNKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGNVEDDLIIFP
DDCEFKRVPQCPSGRVYVLKFKAGSKRLFFWMQEPKTDQDEEHCRKVNEYLNNPP

Sequence of entity 2 (C, D), FASTA

>5V1Z_2 Ubiquitin (chains C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (E, F), FASTA

>5V1Z_3 26S proteasome non-ATPase regulatory subunit 1 (chains E, F)
GPKIEEEEQEPEPPEPFEYIDD

Primary citation

Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism. VanderLinden, R.T., Hemmis, C.W., Yao, T. et al. J Biol Chem (2017) 292:9493-9504. DOI 10.1074/jbc.M117.785287 · 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
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
2KR0 Solution structure of the proteasome ubiquitin receptor Rpn13

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