3PHX: RNA-directed RNA polymerase L

OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15. Determined by X-ray diffraction at 1.6 Å resolution. Released 2 Feb 2011.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Crimean-Congo hemorrhagic fever virus, Homo sapiens
Chains: 2
Atoms: 2,142
Mol. weight: 30.95 kDa
Ligands: NEH, ZN
Released: 2 Feb 2011

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

Secondary structure: helices and β-sheets

3PHX 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	3-6	4
β-strand	10-13	4	1
β-strand	16-19	4	1
β-strand	24	1	2
α-helix	25-28	4
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	86-93	8
β-strand	101	1	3
α-helix	102-112	11
β-strand	116-120	5	1
β-strand	126	1	2
β-strand	129-133	5	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	82-87	6	4
β-strand	93-98	6	4
β-strand	103	1	5
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	4
β-strand	129-130	2	4
α-helix	131-132	2
β-strand	136	1	5
α-helix	137-140	4
β-strand	147-152	6	4
β-strand	155	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-directed RNA polymerase L	A	protein	185	Crimean-Congo hemorrhagic fever virus	Q6TQR6 (AlphaFold model)
Ubiquitin-like protein ISG15	B	protein	79	Homo sapiens	P05161 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3PHX_1 RNA-directed RNA polymerase L (chains A)
GPMDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSY
HYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIII
WTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREALSLMDRVIAV
DQLTS

Sequence of entity 2 (B), FASTA

>3PHX_2 Ubiquitin-like protein ISG15 (chains B)
MDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPL
GEYGLKPLSTVFMNLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
NEH	Ethanamine	C2 H7 N	1
ZN	Zinc ion	Zn	12

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

Primary citation

Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains. Akutsu, M., Ye, Y., Virdee, S. et al. Proc Natl Acad Sci U S A (2011) 108:2228-2233. DOI 10.1073/pnas.1015287108 · 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
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…
3PT2 2.5 Å, Structure of a viral OTU domain protease bound to Ubiquitin

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