PDBsum entry 5z0r

Viral protein

PDB id

5z0r

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Contents

			Protein chains

					442 a.a.

			Ligands

					GLC-GLC ×2

			Waters ×373

PDB id:

5z0r

Links

Name:

Viral protein

Title:

Structural insight into the zika virus capsid encapsulating the viral genome

Structure:

Extracellular solute-binding protein family 1,viral genome protein. Chain: a, b. Engineered: yes. Other_details: the fusion of mbp-tag (unp residues 27-395) and zika virus capsid (unp residues 24-98)

Source:

Escherichia coli. Organism_taxid: 469008. Strain: b / bl21-de3, bl21(de3). Gene: ecbd_4002. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

2.05Å

R-factor:

0.222

R-free:

0.254

Authors:

T.Li,Q.Zhao,X.Yang,C.Chen,K.Yang,C.Wu,T.Zhang,Y.Duan,X.Xue,K.Mi,X.Ji, Z.Wang,H.Yang

Key ref:

T.Li et al. (2018). Structural insight into the Zika virus capsid encapsulating the viral genome. Cell Res, 28, 497-499. PubMed id: 29467384 DOI: 10.1038/s41422-018-0007-9

Date:

20-Dec-17

Release date:

11-Apr-18

PROCHECK

	Headers

	References

Protein chains

P0AEX9 (MALE_ECOLI) - Maltose/maltodextrin-binding periplasmic protein from Escherichia coli (strain K12)

Seq: Struc:					396 a.a. 442 a.a.*

Protein chains

Q32ZE1 (POLG_ZIKV) - Genome polyprotein from Zika virus

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					3419 a.a. 442 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 25 residue positions (black crosses)



		Enzyme reactions

Enzyme class 2:

E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine

5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA	+	S-adenosyl-L- methionine	=	5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA	+	S-adenosyl-L-homocysteine

Enzyme class 3:

E.C.2.1.1.57 - methyltransferase cap1.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺

5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA	+	S-adenosyl-L-methionine	=	5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA	+	S-adenosyl-L-homocysteine	+	H(+)

Enzyme class 4:

E.C.2.7.7.48 - RNA-directed Rna polymerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n)	+	ribonucleoside 5'-triphosphate	=	RNA(n+1)	+	diphosphate

Enzyme class 5:

E.C.3.4.21.91 - flavivirin.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Selective hydrolysis of Xaa-Xaa-|-Xbb bonds in which each of the Xaa can be either Arg or Lys and Xbb can be either Ser or Ala.

Enzyme class 6:

E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

ribonucleoside 5'-triphosphate	+	H2O	=	ribonucleoside 5'-diphosphate	+	phosphate	+	H(+)

Enzyme class 7:

E.C.3.6.4.13 - Rna helicase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP	+	H2O	=	ADP	+	phosphate	+	H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/s41422-018-0007-9	Cell Res 28:497-499 (2018)
PubMed id: 29467384

Structural insight into the Zika virus capsid encapsulating the viral genome.
T.Li, Q.Zhao, X.Yang, C.Chen, K.Yang, C.Wu, T.Zhang, Y.Duan, X.Xue, K.Mi, X.Ji, Z.Wang, H.Yang.

ABSTRACT

No abstract given.