6TXB: Mindy1 mutant

Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin. Determined by X-ray diffraction at 2.18 Å resolution. Released 27 Jan 2021.

Method: X-ray diffraction
Resolution: 2.18 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,634
Mol. weight: 57.87 kDa
Released: 27 Jan 2021

Explore 6TXB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TXB contains 21 α-helices and 40 β-strands across 4 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: 11 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	163-176	14
α-helix	188-200	13
α-helix	203-206	4
β-strand	208-210	3	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
α-helix	307	1
β-strand	311-315	5	7
β-strand	320-326	7	7
β-strand	329-333	5	7
β-strand	336	1	3
α-helix	337-339	3
β-strand	347-350	4	7
β-strand	359-360	2	7
β-strand	366	1	7

Chain D: 4 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	23-34	12
α-helix	38-40	3
β-strand	41-45	5	9
β-strand	48-49	2	9
α-helix	50-51	2
β-strand	55	1	10
α-helix	57-59	3
β-strand	66-71	6	9
β-strand	73-75	3	4

Chain H: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	11
β-strand	12-16	5	11
β-strand	22	1	12
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-45	5	11
β-strand	48-49	2	11
α-helix	50-51	2
β-strand	55	1	12
α-helix	57-59	3
β-strand	66-71	6	11

Chain L: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	13
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-43	3	14
β-strand	50	1	14
β-strand	55	1	13
β-strand	69-71	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase MINDY-1	A	protein	289	Homo sapiens	Q8N5J2 (AlphaFold model)
Polyubiquitin-C	D, H, L	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6TXB_1 Ubiquitin carboxyl-terminal hydrolase MINDY-1 (chains A)
GPLGSPEFPGRLEMEPDFYCVKWIPWKGEQTPIITQSTNGPAALLAIMNILFLQWKVKLP
PQKEVITSDELMAHLGNCLLSIKPQEKSEGLQLNFQQNVDDAMTVLPKLATGLDVNVRFT
GVSDFEYTPECSVFDLLGIPLYHGWLVDPQSPEAVRAVGKLSYNQLVERIITCKHSSDTN
LVTEGLIAEQFLETTAAQLTYHGLCELTAAAKEGELSVFFRNNHFSTMTKHKSHLYLLVT
DQGFLQEEQVVWESLHNVDGDSCFCDSDFHLSHSLGKGPGAEGGSGSPE

Sequence of entity 2 (D, H, L), FASTA

>6TXB_2 Polyubiquitin-C (chains D, H, L)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Abdul Rehman, S.A., Armstrong, L.A., Lange, S.M. et al. Mol Cell (2021) 81:4176-4190.e6. DOI 10.1016/j.molcel.2021.08.024 · 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
5JQS 2.65 Å, Crystal structure of deubiquitinase MINDY-1 in complex with 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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