5V5H: RNA-directed RNA polymerase L

OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.2. Determined by X-ray diffraction at 1.5 Å resolution. Released 10 May 2017.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970), synthetic construct
Chains: 2
Atoms: 2,166
Mol. weight: 32.28 kDa
Ligands: ZN
Released: 10 May 2017

Explore 5V5H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V5H 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: 10 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
α-helix	98-100	3
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: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	4
β-strand	12-17	6	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
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-directed RNA polymerase L	A	protein	174	Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)	Q6TQR6 (AlphaFold model)
Ubiquitin variant CC.2	B	protein	105	synthetic construct

Sequence of entity 1 (A), FASTA

>5V5H_1 RNA-directed RNA polymerase L (chains A)
GPLGSMDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTD
HSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGIT
IIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREAL

Sequence of entity 2 (B), FASTA

>5V5H_2 Ubiquitin variant CC.2 (chains B)
MAHHHHHHVTSLYKKAGSTDYKDDDDKMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK
EGIPPDQQRLIFAGKQLEDGRTLSDYNIRKQSNLYLLWRLGGWKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants. Zhang, W., Bailey-Elkin, B.A., Knaap, R.C.M. et al. PLoS Pathog (2017) 13:e1006372-e1006372. DOI 10.1371/journal.ppat.1006372 · PubMed

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

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…
3PT2 2.5 Å, Structure of a viral OTU domain protease bound to Ubiquitin

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