7NX5: Epstein-Barr Virus protein ZEBRA

Crystal structure of the Epstein-Barr Virus protein ZEBRA (BZLF1, Zta) bound to a methylated DNA duplex. Determined by X-ray diffraction at 2.5 Å resolution. Released 1 Dec 2021.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Epstein-Barr virus (strain B95-8), Human gammaherpesvirus 4
Chains: 8
Atoms: 3,158
Mol. weight: 53.07 kDa
Released: 1 Dec 2021

Explore 7NX5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NX5 contains 10 α-helices and 0 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	176-221	46
α-helix	227-230	4
α-helix	232-234	3

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	178-221	44
α-helix	232-235	4

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	177-221	45
α-helix	227-230	4
α-helix	232-234	3

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	176-221	46
α-helix	227-230	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Trans-activator protein BZLF1	A, B, E, F	protein	63	Epstein-Barr virus (strain B95-8)	P03206 (AlphaFold model)
meZRE2 DNA (bottom strand)	C, G	DNA	19	Human gammaherpesvirus 4
meZRE2 DNA (top strand)	D, H	DNA	19	Human gammaherpesvirus 4

Sequence of entity 1 (A, B, E, F), FASTA

>7NX5_1 Trans-activator protein BZLF1 (chains A, B, E, F)
MLEIKRYKNRVASRKSRAKFKQLLQHYREVAAAKSSENDRLRLLLKQMCPSLDVDSIIPR
TPD

Sequence of entity 2 (C, G), FASTA

>7NX5_2 meZRE2 DNA (bottom strand) (chains C, G)
TACTTCATCGCTCAGTGCT

Sequence of entity 3 (D, H), FASTA

>7NX5_3 meZRE2 DNA (top strand) (chains D, H)
AAGCACTGAGCGATGAAGT

Primary citation

Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1. Bernaudat, F., Gustems, M., Gunther, J. et al. Nucleic Acids Res (2022) 50:490-511. DOI 10.1093/nar/gkab1183 · PubMed

Other PDB entries of the same protein (UniProt P03206 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3SPV 1.3 Å, Crystal structure of a peptide-HLA complex
3VFN 1.5 Å, crystal structure of HLA B*3508LPEP151A, HLA mutant Ala151
1ZSD 1.7 Å, Crystal Structure Of HLA-B*3501 Presenting an 11-Mer EBV Antigen EPLPQGQLTAY
3VFO 1.7 Å, crystal structure of HLA B*3508 LPEP157A, HLA mutant Ala157
2AXF 1.8 Å, The Immunogenicity of a Viral Cytotoxic T Cell Epitope is controlled by its MHC-bound…
3VFP 1.85 Å, crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158
3VFR 1.85 Å, crystal structure of HLA B*3508LPEP-P4Ala, peptide mutant P4-ala
2AXG 2.0 Å, The Immunogenicity of a Viral Cytotoxic T Cell Epitope is controlled by its MHC-bound…
3KWW 2.18 Å, Crystal structure of the 'restriction triad' mutant of HLA B*3508, beta-2-microglobulin…
2C9L 2.25 Å, Structure of the Epstein-Barr virus ZEBRA protein
5SZX 2.25 Å, Epstein-Barr virus Zta DNA binding domain homodimer in complex with methylated DNA
2AK4 2.5 Å, Crystal Structure of SB27 TCR in complex with HLA-B*3508-13mer peptide

Browse structure collections

About this viewer

MolViewer shows 7NX5 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.