3PHW: RNA-directed RNA polymerase L

OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin. Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Feb 2011.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Crimean-Congo hemorrhagic fever virus strain IbAr10200, Homo sapiens
Chains: 8
Atoms: 8,055
Mol. weight: 118.31 kDa
Ligands: NEH
Released: 2 Feb 2011

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

Secondary structure: helices and β-sheets

3PHW contains 48 α-helices and 70 β-strands across 8 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	9	1
β-strand	10-13	4	1
β-strand	16-19	4	1
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	2
α-helix	102-112	11
β-strand	116-120	5	1
β-strand	129-133	5	1
β-strand	142-147	6	1
β-strand	151-157	7	1
α-helix	159-161	3

Chains B, D and H: 4 helices, 8 β-strands

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

Chain C: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	10-13	4	5
β-strand	16-19	4	5
β-strand	24	1	6
α-helix	25-28	4
β-strand	29-32	4	5
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	7
α-helix	102-112	11
β-strand	116-120	5	5
β-strand	126	1	6
β-strand	129-133	5	5
β-strand	142-147	6	5
β-strand	151-157	7	5

Chain E: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	10
β-strand	16-19	4	10
β-strand	24	1	11
α-helix	25-28	4
β-strand	29-32	4	10
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
α-helix	98-100	3
β-strand	101	1	12
α-helix	102-111	10
β-strand	116-120	5	10
β-strand	126	1	11
β-strand	129-133	5	10
β-strand	142-147	6	10
β-strand	151-157	7	10

Chain F: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	13
β-strand	12-16	5	13
β-strand	22	1	14
α-helix	23-34	12
β-strand	41-45	5	13
β-strand	48-49	2	13
α-helix	50-51	2
β-strand	55	1	14
α-helix	57-59	3
β-strand	66-71	6	13
β-strand	74	1	12

Chain G: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	15
β-strand	16-19	4	15
β-strand	24	1	16
α-helix	25-28	4
β-strand	29-32	4	15
α-helix	40-49	10
α-helix	58-72	15
α-helix	77-81	5
α-helix	86-94	9
β-strand	101	1	17
α-helix	102-112	11
β-strand	116-121	6	15
β-strand	126	1	16
β-strand	127-133	7	15
β-strand	142-147	6	15
β-strand	151-157	7	15
α-helix	159-161	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-directed RNA polymerase L	A, C, E, G	protein	185	Crimean-Congo hemorrhagic fever virus strain IbAr10200	Q6TQR6 (AlphaFold model)
Ubiquitin-40S ribosomal protein S27a	B, D, F, H	protein	75	Homo sapiens	P62979 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3PHW_1 RNA-directed RNA polymerase L (chains A, C, E, G)
GPMDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSY
HYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIII
WTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREALSLMDRVIAV
DQLTS

Sequence of entity 2 (B, D, F, H), FASTA

>3PHW_2 Ubiquitin-40S ribosomal protein S27a (chains B, D, F, H)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
NEH	Ethanamine	C2 H7 N	4

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
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…
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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