5MN9: MINDY-1 tMIU

Crystal structure of MINDY-1 tMIU in complex with K48-diUb. Determined by X-ray diffraction at 2.05 Å resolution. Released 25 Jan 2017.

Method: X-ray diffraction
Resolution: 2.05 Å
Organisms: Bos taurus, Homo sapiens
Chains: 3
Atoms: 1,335
Mol. weight: 22.09 kDa
Released: 25 Jan 2017

Explore 5MN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MN9 contains 9 α-helices and 14 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.

Chains A and B: 4 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
β-strand	66-71	6	1

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	411-425	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-40S ribosomal protein S27a	A, B	protein	76	Bos taurus	P62992 (AlphaFold model)
Ubiquitin carboxyl-terminal hydrolase MINDY-1	C	protein	44	Homo sapiens	Q8N5J2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5MN9_1 Ubiquitin-40S ribosomal protein S27a (chains A, B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (C), FASTA

>5MN9_2 Ubiquitin carboxyl-terminal hydrolase MINDY-1 (chains C)
GPLGSQVDQDYLIALSLQQQQPRGPLGLTDLELAQQLQQEEYQQ

Primary citation

A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. Kristariyanto, Y.A., Abdul Rehman, S.A., Weidlich, S. et al. EMBO Rep (2017) 18:392-402. DOI 10.15252/embr.201643205 · PubMed

Other PDB entries of the same protein (UniProt P62992 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q01 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2
5XVE 1.24 Å, Crystal structure of human USP2 C276S mutant in complex with ubiquitin
4M0W 1.4 Å, Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin
4Y1H 1.4 Å, Crystal structure of K33 linked tri-Ubiquitin
6E2B 1.45 Å, Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3)
5XU8 1.81 Å, Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine
5BZ0 2.1 Å, Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin
7F0U 2.2 Å, porcine epidemic diarrhea virus papain-like protease 2 C44S mutant in complex with mono…
4Z9S 2.3 Å, Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin
5FER 2.34 Å, Complex of TRIM25 RING with UbcH5-Ub
5JQS 2.65 Å, Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin
6DJW 3.8 Å, Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex

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