6SAK: OTULINcat C129A - SNX27 PDZ domain complex

Structure of the OTULINcat C129A - SNX27 PDZ domain complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Oct 2019.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,026
Mol. weight: 85.64 kDa
Released: 2 Oct 2019

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

Secondary structure: helices and β-sheets

6SAK contains 42 α-helices and 42 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: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	82	1	1
α-helix	83-85	3
β-strand	86-87	2	2
α-helix	88-95	8
α-helix	101-113	13
β-strand	117-122	6	2
β-strand	123	1	1
α-helix	124	1
α-helix	129-140	12
α-helix	147-150	4
α-helix	152-156	5
α-helix	157-164	8
α-helix	166-170	5
α-helix	181-183	3
α-helix	184-203	20
α-helix	208-218	11
α-helix	223-249	27
α-helix	255-262	8
α-helix	269-275	7
α-helix	277-279	3
β-strand	280	1	3
β-strand	284	1	3
α-helix	290-297	8
β-strand	301-306	6	2
α-helix	307-309	3
α-helix	313-315	3
β-strand	316-319	4	2
β-strand	329-334	6	2
β-strand	340-346	7	2
β-strand	347-351	5	4

Chain B: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	82	1	5
α-helix	83-85	3
β-strand	86-87	2	6
α-helix	88-95	8
α-helix	101-113	13
β-strand	117-122	6	6
β-strand	123	1	5
α-helix	124	1
α-helix	129-140	12
α-helix	147-150	4
α-helix	152-156	5
α-helix	157-164	8
α-helix	166-170	5
α-helix	185-204	20
α-helix	208-218	11
α-helix	223-248	26
α-helix	255-262	8
α-helix	264-266	3
α-helix	269-272	4
α-helix	273-277	5
β-strand	280	1	7
β-strand	284	1	7
α-helix	288-298	11
β-strand	301-306	6	6
α-helix	307-309	3
β-strand	316-319	4	6
β-strand	329-334	6	6
β-strand	340-346	7	6
β-strand	347-351	5	8

Chain C: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	41-47	7	4
β-strand	49	1	9
β-strand	52	1	9
β-strand	55-60	6	4
β-strand	68-70	3	10
β-strand	73-75	3	10
β-strand	79-84	6	4
α-helix	89-93	5
α-helix	99	1
β-strand	100-104	5	4
β-strand	107-108	2	4
α-helix	114-123	10
β-strand	127-133	7	4

Chain D: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	41-47	7	8
β-strand	49	1	11
β-strand	52	1	11
β-strand	55-60	6	8
β-strand	68-70	3	12
β-strand	73-75	3	12
β-strand	80-84	5	8
α-helix	89-93	5
β-strand	100-104	5	8
β-strand	107-108	2	8
α-helix	114-123	10
β-strand	127-133	7	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin thioesterase otulin	A, B	protein	275	Homo sapiens	Q96BN8 (AlphaFold model)
Sorting nexin-27	C, D	protein	96	Homo sapiens	Q96L92 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6SAK_1 Ubiquitin thioesterase otulin (chains A, B)
GPLSVAPEMDIMDYCKKEWRGNTQKATCMKMGYEEVSQKFTSIRRVRGDNYAALRATLFQ
AMSQAVGLPPWLQDPELMLLPEKLISKYNWIKQWKLGLKFDGKNEDLVDKIKESLTLLRK
KWAGLAEMRTAEARQIACDELFTNEAEEYSLYEAVKFLMLNRAIELYNDKEKGKEVPFFS
VLLFARDTSNDPGQLLRNHLNQVGHTGGLEQVEMFLLAYAVRHTIQVYRLSKYNTEEFIT
VYPTDPPKDWPVVTLIAEDDRHYNIPVRVCEETSL

Sequence of entity 2 (C, D), FASTA

>6SAK_2 Sorting nexin-27 (chains C, D)
GPRVVRIVKSESGYGFNVRGQVSEGGQLRSINGELYAPLQHVSAVLPGGAADRAGVRKGD
RILEVNHVNVEGATHKQVVDLIRAGEKELILTVLSV

Primary citation

Regulation of the endosomal SNX27-retromer by OTULIN. Stangl, A., Elliott, P.R., Pinto-Fernandez, A. et al. Nat Commun (2019) 10:4320-4320. DOI 10.1038/s41467-019-12309-z · PubMed

Other PDB entries of the same protein (UniProt Q96BN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZNV 1.3 Å, Crystal structure of the OTU domain of OTULIN at 1.3 Angstroms.
3ZNX 1.35 Å, Crystal structure of the OTU domain of OTULIN D336A mutant
4KSJ 1.6 Å, Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom
6I9C 1.77 Å, Structure of the OTU domain of OTULIN G281R mutant
3ZNZ 1.9 Å, Crystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin
9LZX 2.0 Å, Crystal structure of the OTU domain of OTULIN in complex with 11B6
4OYK 2.0 Å, Structure of HOIP PUB domain bound to OTULIN PIM
4KSK 2.4 Å, Gumby/Fam105B in complex with ubiquitin
4P0B 2.7 Å, Crystal structure of HOIP PUB domain in complex with OTULIN PIM
4KSL 2.83 Å, Gumby/Fam105B in complex with linear di-ubiquitin
5OE7 2.95 Å, Structure of OTULIN bound to the Met1-linked diubiquitin activity probe

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