3PT2: Viral OTU domain protease

Structure of a viral OTU domain protease bound to Ubiquitin. Determined by X-ray diffraction at 2.5 Å resolution. Released 19 Jan 2011.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Crimean-Congo hemorrhagic fever virus, Homo sapiens
Chains: 2
Atoms: 2,041
Mol. weight: 30.44 kDa
Ligands: 4LJ
Released: 19 Jan 2011

Explore 3PT2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PT2 contains 13 α-helices and 18 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	0-5	6
β-strand	10-13	4	1
β-strand	16-19	4	1
β-strand	24	1	2
α-helix	25-27	3
β-strand	29-32	4	1
α-helix	40-49	10
α-helix	58-72	15
α-helix	73-75	3
α-helix	79-82	4
α-helix	86-94	9
β-strand	101	1	3
α-helix	102-112	11
β-strand	116-121	6	1
β-strand	126	1	2
β-strand	127-133	7	1
β-strand	142-147	6	1
β-strand	151-157	7	1
α-helix	159-161	3

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
α-helix	57-59	3
β-strand	66-71	6	4
β-strand	74	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA polymerase	A	protein	187	Crimean-Congo hemorrhagic fever virus	Q6TQR6 (AlphaFold model)
Ubiquitin B	B	protein	75	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3PT2_1 RNA polymerase (chains A)
GPGMDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHS
YHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITII
IWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREALSLMDRVIA
VDQLTSS

Sequence of entity 2 (B), FASTA

>3PT2_2 Ubiquitin B (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
4LJ	1.7.6 3-bromanylpropan-1-amine	C3 H8 Br N	1

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

Primary citation

Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease. James, T.W., Frias-Staheli, N., Bacik, J.P. et al. Proc Natl Acad Sci U S A (2011) 108:2222-2227. DOI 10.1073/pnas.1013388108 · PubMed

Other PDB entries of the same protein (UniProt Q6TQR6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5V5H 1.5 Å, OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.2
3PHX 1.6 Å, OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15
3PRP 1.7 Å, Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic…
3PHW 2.0 Å, OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin
5V5G 2.1 Å, OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.4
3PHU 2.2 Å, OTU Domain of Crimean Congo Hemorrhagic Fever Virus
5V5I 2.2 Å, OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.1
3PRM 2.3 Å, Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic…
3PSE 2.3 Å, Structure of a viral OTU domain protease bound to interferon-stimulated gene 15 (ISG15)
3ZNH 2.3 Å, Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl.
9T0E 2.3 Å, Structure of Crimean Congo hemorrhagic fever virus (CCHFV) L protein bound to 5' vRNA…
22TH 2.5 Å, Cryo-EM structure of Crimean-Congo hemorrhagic fever virus RNA polymerase in complex…

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