5JQS: Deubiquitinase MINDY-1

Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin. Determined by X-ray diffraction at 2.65 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Homo sapiens, Bos taurus
Chains: 2
Atoms: 3,157
Mol. weight: 41.08 kDa
Ligands: DIO, AYE
Released: 22 Jun 2016

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

Secondary structure: helices and β-sheets

5JQS contains 12 α-helices and 28 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: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	113-115	3	1
β-strand	116-121	6	2
β-strand	124-129	6	2
β-strand	131	1	3
α-helix	137-148	12
β-strand	160-162	3	1
α-helix	163-174	12
α-helix	188-206	19
β-strand	209	1	4
β-strand	212	1	5
β-strand	213	1	6
β-strand	220	1	5
α-helix	224-231	8
β-strand	236-237	2	7
β-strand	239	1	8
α-helix	247-253	7
β-strand	257	1	6
α-helix	258-270	13
α-helix	274-289	16
β-strand	294	1	8
α-helix	296-305	10
β-strand	311-316	6	7
β-strand	319-326	8	7
β-strand	329-333	5	7
β-strand	336	1	3
α-helix	337-339	3
β-strand	347-349	3	7
β-strand	359-360	2	7
β-strand	366	1	7

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	12-16	5	9
β-strand	22	1	10
α-helix	23-31	9
α-helix	38-40	3
β-strand	41-45	5	9
β-strand	48-50	3	9
β-strand	55	1	10
α-helix	57-59	3
β-strand	66-71	6	9
β-strand	74	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein FAM63A	A	protein	289	Homo sapiens	Q8N5J2 (AlphaFold model)
Ubiquitin-40S ribosomal protein S27a	D	protein	76	Bos taurus	P62992 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5JQS_1 Protein FAM63A (chains A)
GPLGSPEFPGRLEMEPDFYCVKWIPWKGEQTPIITQSTNGPCPLLAIMNILFLQWKVKLP
PQKEVITSDELMAHLGNCLLSIKPQEKSEGLQLNFQQNVDDAMTVLPKLATGLDVNVRFT
GVSDFEYTPECSVFDLLGIPLYHGWLVDPQSPEAVRAVGKLSYNQLVERIITCKHSSDTN
LVTEGLIAEQFLETTAAQLTYHGLCELTAAAKEGELSVFFRNNHFSTMTKHKSHLYLLVT
DQGFLQEEQVVWESLHNVDGDSCFCDSDFHLSHSLGKGPGAEGGSGSPE

Sequence of entity 2 (D), FASTA

>5JQS_2 Ubiquitin-40S ribosomal protein S27a (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
DIO	1,4-diethylene dioxide	C4 H8 O2	1
AYE	prop-2-en-1-amine	C3 H7 N	1

Water and common crystallization additives (CL, SO4) are not listed.

Primary citation

MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Abdul Rehman, S.A., Kristariyanto, Y.A., Choi, S.Y. et al. Mol Cell (2016) 63:146-155. DOI 10.1016/j.molcel.2016.05.009 · PubMed

Other PDB entries of the same protein (UniProt Q8N5J2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MN9 2.05 Å, Crystal structure of MINDY-1 tMIU in complex with K48-diUb
6TUV 2.16 Å, Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin
6TXB 2.18 Å, Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin
5JKN 3.0 Å, Crystal structure of deubiquitinase MINDY-1
6YJG 3.28 Å, Crystal structure of MINDY1 mutant-Y114F
6Y6R 3.32 Å, Crystal structure of MINDY1 T335D mutant
6Z90 3.59 Å, Crystal structure of MINDY1 mutant-P138A

Browse structure collections

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