8XPN: USP8 from Biortus

The Crystal Structure of USP8 from Biortus. Determined by X-ray diffraction at 2.1 Å resolution. Released 6 Mar 2024.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,768
Mol. weight: 130.58 kDa
Ligands: ZN
Released: 6 Mar 2024

Explore 8XPN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XPN contains 42 α-helices and 69 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.

Chain A: 15 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	767	1
β-strand	768-769	2	1
β-strand	778-779	2	1
α-helix	786-796	11
α-helix	801-806	6
α-helix	810-813	4
α-helix	825-839	15
β-strand	842-845	4	1
α-helix	848-857	10
α-helix	859-861	3
α-helix	869-883	15
α-helix	903-917	15
α-helix	921-926	6
β-strand	928-936	9	2
β-strand	942-945	4	2
β-strand	948-949	2	2
β-strand	952-954	3	3
β-strand	961-963	3	4
α-helix	964-971	8
β-strand	975-977	3	2
α-helix	979-981	3
α-helix	982	1
β-strand	983-985	3	5
β-strand	990-992	3	5
β-strand	994-1002	9	2
β-strand	1006-1011	6	3
β-strand	1014	1	6
β-strand	1023	1	6
β-strand	1027-1029	3	4
β-strand	1035	1	7
α-helix	1038-1040	3
β-strand	1041	1	2
β-strand	1051	1	7
β-strand	1052-1060	9	3
β-strand	1067-1074	8	3
β-strand	1079-1084	6	3
β-strand	1087-1090	4	3
α-helix	1093-1095	3
β-strand	1101-1107	7	3

Chain B: 14 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	768-769	2	8
β-strand	778-779	2	8
α-helix	786-796	11
α-helix	801-806	6
α-helix	809-813	5
α-helix	825-839	15
β-strand	842-845	4	8
α-helix	848-857	10
α-helix	859-861	3
α-helix	869-883	15
α-helix	903-917	15
α-helix	921-926	6
β-strand	928-936	9	9
β-strand	942-945	4	9
β-strand	948-949	2	9
β-strand	952-954	3	10
α-helix	955-956	2
β-strand	961-963	3	11
α-helix	964-971	8
β-strand	975-977	3	9
α-helix	979-981	3
β-strand	983-985	3	12
β-strand	990-992	3	12
β-strand	994-1002	9	9
β-strand	1006-1011	6	10
β-strand	1014-1016	3	13
β-strand	1021-1023	3	13
β-strand	1027-1029	3	11
β-strand	1035	1	14
α-helix	1038-1040	3
β-strand	1041	1	9
β-strand	1051	1	14
β-strand	1052-1060	9	10
β-strand	1067-1074	8	10
β-strand	1079-1084	6	10
β-strand	1087-1090	4	10
α-helix	1093-1096	4
β-strand	1101-1107	7	10

Chain C: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	759-765	7
β-strand	768-769	2	15
β-strand	778-779	2	15
α-helix	786-796	11
α-helix	801-806	6
α-helix	810-813	4
α-helix	825-839	15
β-strand	842-845	4	15
α-helix	848-857	10
α-helix	859-861	3
α-helix	869-883	15
α-helix	903-917	15
α-helix	921-926	6
β-strand	928-935	8	16
β-strand	942-945	4	16
β-strand	948-949	2	16
β-strand	952-954	3	17
β-strand	961-963	3	18
α-helix	964-972	9
β-strand	995-1002	8	16
β-strand	1006-1011	6	17
β-strand	1014-1016	3	19
β-strand	1021-1023	3	19
β-strand	1027-1029	3	18
β-strand	1035	1	20
α-helix	1038-1040	3
β-strand	1041	1	16
β-strand	1051	1	20
β-strand	1052-1060	9	17
β-strand	1067-1074	8	17
β-strand	1079-1084	6	17
β-strand	1087-1090	4	17
α-helix	1093-1096	4
β-strand	1101-1107	7	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 8	A, B, C	protein	377	Homo sapiens	P40818 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8XPN_1 Ubiquitin carboxyl-terminal hydrolase 8 (chains A, B, C)
PTVTPTVNRENKPTCYPKAEISRLSASQIRNLNPVFGGSGPALTGLRNLGNTCYMNSILQ
CLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKALWTGQYRYISPKDFKIT
IGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEENNDHLDDFKAAEHAWQK
HKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSLPLASTSKCTLQDCLRLFSK
EEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPLE
NLDLSQYVIGPKNNLKKYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHEVSDISV
SSVKSSAAYILFYTSLG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Water and common crystallization additives (PEG, EDO) are not listed.

Primary citation

The Crystal Structure of USP8 from Biortus. Wang, F., Cheng, W., Yuan, Z. et al. To be published.

Other PDB entries of the same protein (UniProt P40818 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6F09 1.59 Å, Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide
8ADM 1.7 Å, Ternary complex of 14-3-3 sigma, Usp8pS718 phosphopeptide and small molecule stabilizer
2GFO 2.0 Å, Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-terminal Hydrolase 8
2A9U 2.1 Å, Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8)
2GWF 2.3 Å, Structure of a USP8-NRDP1 complex
3N3K 2.6 Å, The catalytic domain of USP8 in complex with a USP8 specific inhibitor
8Y9A 3.1 Å, The Crystal Structure of USP8 from Biortus.
1WHB Solution structure of the Rhodanese-like domain in human ubiquitin specific protease 8…

Browse structure collections

About this viewer

MolViewer shows 8XPN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.