3PRM: RNA-directed RNA polymerase L

Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin. Determined by X-ray diffraction at 2.3 Å resolution. Released 26 Jan 2011.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Crimean-Congo hemorrhagic fever virus, Homo sapiens
Chains: 4
Atoms: 4,168
Mol. weight: 58.43 kDa
Released: 26 Jan 2011

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

Secondary structure: helices and β-sheets

3PRM contains 27 α-helices and 38 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: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
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	77-81	5
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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	11	1	5
β-strand	12-16	5	4
β-strand	22	1	6
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	6
α-helix	57-59	3
β-strand	66-71	6	4
β-strand	74	1	3

Chain C: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	10-13	4	7
β-strand	16-19	4	7
β-strand	22	1	5
β-strand	24	1	8
α-helix	25-28	4
β-strand	29-32	4	7
α-helix	40-47	8
α-helix	58-72	15
α-helix	73-75	3
α-helix	77-81	5
α-helix	86-94	9
α-helix	98-100	3
β-strand	101	1	9
α-helix	102-111	10
β-strand	116-121	6	7
β-strand	126	1	8
β-strand	127-133	7	7
β-strand	142-147	6	7
β-strand	151-157	7	7
α-helix	159-161	3

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	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	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-directed RNA polymerase L	A, C	protein	178	Crimean-Congo hemorrhagic fever virus	Q6TQR6 (AlphaFold model)
Polyubiquitin-B (Fragment)	B, D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3PRM_1 RNA-directed RNA polymerase L (chains A, C)
MDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHY
IKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWT
VAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREALSGSHHHHHH

Sequence of entity 2 (B, D), FASTA

>3PRM_2 Polyubiquitin-B (Fragment) (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGX

Primary citation

Structural analysis of a viral ovarian tumor domain protease from the crimean-congo hemorrhagic Fever virus in complex with covalently bonded ubiquitin. Capodagli, G.C., McKercher, M.A., Baker, E.A. et al. J Virol (2011) 85:3621-3630. DOI 10.1128/JVI.02496-10 · 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
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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