4RF0: ORF1ab protein

Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P6522). Determined by X-ray diffraction at 2.8 Å resolution. Released 22 Oct 2014.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Human betacoronavirus 2c Jordan-N3/2012, Homo sapiens
Chains: 2
Atoms: 3,125
Mol. weight: 45.56 kDa
Ligands: 3CN, ZN
Released: 22 Oct 2014

Explore 4RF0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RF0 contains 16 α-helices and 30 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: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	1485-1490	6	1
β-strand	1497-1501	5	1
α-helix	1507-1510	4
β-strand	1514	1	2
β-strand	1515	1	3
β-strand	1520	1	3
β-strand	1534-1536	3	1
β-strand	1537	1	2
α-helix	1543-1553	11
α-helix	1560-1570	11
α-helix	1571-1573	3
β-strand	1576-1578	3	4
β-strand	1583-1585	3	4
α-helix	1586-1587	2
α-helix	1592-1601	10
β-strand	1607-1609	3	5
α-helix	1612-1621	10
α-helix	1627-1636	10
α-helix	1639-1640	2
α-helix	1647-1655	9
β-strand	1658-1660	3	5
β-strand	1665-1672	8	6
β-strand	1676-1683	8	6
α-helix	1685-1687	3
β-strand	1689-1691	3	7
α-helix	1696-1700	5
α-helix	1702	1
β-strand	1703-1706	4	6
β-strand	1712-1722	11	6
β-strand	1725-1737	13	7
β-strand	1746-1751	6	7
β-strand	1759-1766	8	7
β-strand	1769-1773	5	7
β-strand	1778-1779	2	7
β-strand	1783-1793	11	7
β-strand	1796-1799	4	6

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	8
β-strand	48-49	2	8
β-strand	55	1	9
β-strand	66-71	6	8
α-helix	72-73	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ORF1ab protein	A	protein	324	Human betacoronavirus 2c Jordan-N3/2012	M4STU1
Ubiquitin-60S ribosomal protein L40	B	protein	75	Homo sapiens	P62987 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4RF0_1 ORF1ab protein (chains A)
TQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLAD
NLTADETKALKELYGPVDPTFLHRFYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIM
TLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAE
LCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVE
HTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVS
KTSDWKCKVTDVLFPGQKYSSDCN

Sequence of entity 2 (B), FASTA

>4RF0_2 Ubiquitin-60S ribosomal protein L40 (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
3CN	3-aminopropane	C3 H9 N	1
ZN	Zinc ion	Zn	1

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

Primary citation

Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression. Bailey-Elkin, B.A., Knaap, R.C., Johnson, G.G. et al. J Biol Chem (2014) 289:34667-34682. DOI 10.1074/jbc.M114.609644 · PubMed

Other PDB entries of the same protein (UniProt M4STU1), best resolution first:

4RF1 2.15 Å, Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like…
5W8U 2.41 Å, Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain…
5W8T 2.76 Å, Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain…
4REZ 2.8 Å, Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease

Browse structure collections

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