4I6N: Trichinella spiralis UCH37 catalytic domain

Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl methyl ester. Determined by X-ray diffraction at 1.7 Å resolution. Released 29 May 2013.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Trichinella spiralis, Homo sapiens
Chains: 4
Atoms: 5,022
Mol. weight: 70.07 kDa
Ligands: DTT, GVE
Released: 29 May 2013

Explore 4I6N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4I6N contains 32 α-helices and 36 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: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	-2-1	4
β-strand	10	1	1
α-helix	13-22	10
β-strand	26	1	2
β-strand	28-33	6	3
α-helix	41-43	3
α-helix	44	1
β-strand	46-54	9	3
α-helix	57-61	5
β-strand	63	1	4
α-helix	68-72	5
α-helix	85-94	10
β-strand	103	1	2
α-helix	105-115	11
α-helix	120-128	9
α-helix	131-139	9
α-helix	154-156	3
β-strand	160-168	9	3
β-strand	171-175	5	3
β-strand	183-187	5	3
α-helix	194-206	13
β-strand	217-223	7	3

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
β-strand	12-16	5	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-71	6	5
β-strand	74	1	1

Chain C: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	7
α-helix	13-22	10
β-strand	26	1	8
β-strand	28-33	6	9
α-helix	41-43	3
α-helix	44	1
β-strand	46-54	9	9
α-helix	57-61	5
α-helix	68-73	6
α-helix	85-94	10
β-strand	103	1	8
α-helix	105-115	11
β-strand	118	1	4
α-helix	120-128	9
α-helix	131-138	8
α-helix	154-156	3
β-strand	160-168	9	9
β-strand	171-175	5	9
β-strand	183-187	5	9
α-helix	188-189	2
α-helix	195-207	13
β-strand	216-223	8	9

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	12-16	5	10
β-strand	22	1	11
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	10
β-strand	48-49	2	10
α-helix	50-51	2
β-strand	55	1	11
α-helix	57-59	3
β-strand	66-71	6	10
β-strand	74	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-hydrolase	A, C	protein	231	Trichinella spiralis	A0ABR3K354
Ubiquitin	B, D	protein	75	Homo sapiens	F5H388 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4I6N_1 Ubiquitin carboxyl-hydrolase (chains A, C)
GPLGSMAEGNWCLIESDPGIFTEMIHGFGCTGLQVEELVVLDESIEHLKPIHGFIFLFRW
LKKEMRKEVDDSPQTCTDVYFSQQVIQNACASQALINLLLNCDHPDVDLGPTLKEFKDFT
YDLDSASRGLCLTNSEKIRAVHNSFGRQQLFEIDDQQKLDEEDVFHFVTYVPVNDGVYEL
DGLRAAPLRLGTVASDGDWTEVAIKAIKEKIKNYGESEVRFNLMAVISDQK

Sequence of entity 2 (B, D), FASTA

>4I6N_2 Ubiquitin (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
DTT	2,3-dihydroxy-1,4-dithiobutane	C4 H10 O2 S2	1
GVE	Methyl 4-aminobutanoate	C5 H11 N O2	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Stabilization of an Unusual Salt Bridge in Ubiquitin by the Extra C-Terminal Domain of the Proteasome-Associated Deubiquitinase UCH37 as a Mechanism of Its Exo Specificity. Morrow, M.E., Kim, M.I., Ronau, J.A. et al. Biochemistry (2013) 52:3564-3578. DOI 10.1021/bi4003106 · PubMed

Other PDB entries of the same protein (UniProt A0ABR3K354), best resolution first:

4IG7 2.0 Å, Crystal structure of Trichinella spiralis UCH37 bound to Ubiquitin vinyl methyl ester

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