5YMY: Complex between Rpn13 and K48-diUb

The structure of the complex between Rpn13 and K48-diUb. Determined by solution NMR. Released 13 Mar 2019.

Method: Solution NMR
Organism: Homo sapiens
Chains: 3
Atoms: 2,144
Mol. weight: 33.92 kDa
Released: 13 Mar 2019

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

Secondary structure: helices and β-sheets

5YMY contains 11 α-helices and 24 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-71	6	1

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-70	5	3

Chain C: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	5
β-strand	28-30	3	6
β-strand	31-34	4	7
β-strand	37-40	4	7
β-strand	45-51	7	5
β-strand	57-63	7	5
β-strand	69-74	6	5
β-strand	80-84	5	6
β-strand	93-98	6	6
β-strand	104-109	6	6
α-helix	117-129	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
Ubiquitin	B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
Proteasomal ubiquitin receptor ADRM1	C	protein	150	Homo sapiens	Q16186 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YMY_1 Ubiquitin (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (B), FASTA

>5YMY_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>5YMY_3 Proteasomal ubiquitin receptor ADRM1 (chains C)
MTTSGALFPSLVPGSRGASNKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFC
WKDRTSGNVEDDLIIFPDDCEFKRVPQCPSGRVYVLKFKAGSKRLFFWMQEPKTDQDEEH
CRKVNEYLNNPPMPGALGASGSSGHELSAL

Primary citation

Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13. Liu, Z., Dong, X., Yi, H.W. et al. Cell Discov (2019) 5:19-19. DOI 10.1038/s41421-019-0089-7 · PubMed

Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
5DK8 1.32 Å, Human ubiquitin in the P1 space group
7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

Browse structure collections

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