5YN5: MERS-CoV nsp10/nsp16 complex

Crystal structure of MERS-CoV nsp10/nsp16 complex. Determined by X-ray diffraction at 1.96 Å resolution. Released 5 Dec 2018.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Human betacoronavirus 2c EMC/2012
Chains: 2
Atoms: 3,321
Mol. weight: 48.77 kDa
Ligands: ZN
Released: 5 Dec 2018

Explore 5YN5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YN5 contains 24 α-helices and 23 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: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	8-10	3	1
α-helix	13-16	4
α-helix	34-36	3
α-helix	37-39	3
α-helix	42-54	13
β-strand	66-70	5	1
β-strand	74	1	2
β-strand	78	1	2
α-helix	80-88	9
β-strand	94-99	6	1
β-strand	109-112	4	1
α-helix	115-117	3
β-strand	118-120	3	3
β-strand	124-129	6	1
α-helix	149-159	11
β-strand	161-162	2	1
β-strand	163	1	4
β-strand	164-171	8	1
α-helix	178-183	6
α-helix	184-186	3
β-strand	187-195	9	1
α-helix	196-198	3
β-strand	204-211	8	1
α-helix	221-234	14
α-helix	242-245	4
α-helix	252-253	2
β-strand	259-260	2	4
α-helix	264-266	3
α-helix	269-276	8
β-strand	281-282	2	4
β-strand	290-292	3	3

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-16	9
α-helix	23-32	10
α-helix	35-38	4
β-strand	43	1	5
α-helix	44-45	2
β-strand	55-56	2	5
β-strand	65-69	5	5
α-helix	71-73	3
α-helix	75-78	4
β-strand	96-100	5	5
α-helix	101-103	3
α-helix	107-113	7
β-strand	116	1	6
β-strand	123	1	6
β-strand	126-127	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
nsp16 protein	A	protein	303	Human betacoronavirus 2c EMC/2012	K0BWD0 (AlphaFold model)
nsp10 protein	B	protein	140	Human betacoronavirus 2c EMC/2012	K4LC41 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YN5_1 nsp16 protein (chains A)
ASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMPRGVHMNIAKYMQLCQYLNTCTLA
VPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRV
GQQVDLVISDMYDPTTKNVTGSNESKALFFTYLCNLINNNLALGGSVAIKITEHSWSVEL
YELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLS
TYSLFDLSKFQLKLKGTPVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTDVLVNTYR
KLR

Sequence of entity 2 (B), FASTA

>5YN5_2 nsp10 protein (chains B)
AGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKTGTGIAISVKPE
STADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVC
QYWIGYGCNCDSLRQAALPQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex. Wei, S.M., Yang, L., Ke, Z.H. et al. To be published.

Other PDB entries of the same protein (UniProt K0BWD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YNM 1.68 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAM and m7GpppA
5YNF 1.79 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to m7GpppA
5YNN 1.86 Å, Crystal structure of MERS-CoV nsp16/nsp10complex bound to sinefungin and m7GpppG
5YN6 1.95 Å, Crystal structure of MERS-CoV nsp10/nsp16 complex bound to SAM
5YNQ 1.96 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH and m7GpppG
5YNO 1.96 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH and m7GpppA
5YN8 1.97 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH
5YNB 1.98 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to Sinefungin
5YNJ 2.04 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to m7GpppG
5YNI 2.07 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAM and m7GpppG
5YNP 2.27 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to sinefungin and m7GpppA
6BI8 2.29 Å, X-ray structure of MERS coronavirus papain-like protease in complex with human ISG15

Browse structure collections

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