6NPI: Epstein-Barr Virus Nuclear Antigen-1, EBNA1

Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments. Determined by X-ray diffraction at 1.5 Å resolution. Released 20 Mar 2019.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Epstein-Barr virus (strain B95-8)
Chains: 2
Atoms: 2,623
Mol. weight: 31.11 kDa
Ligands: KW1, 60Q
Released: 20 Mar 2019

Explore 6NPI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NPI contains 16 α-helices and 10 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: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	477-489	13
β-strand	503-511	9	1
α-helix	514-527	14
β-strand	532-533	2	1
α-helix	534-536	3
β-strand	537-540	4	1
α-helix	541	1
α-helix	552-554	3
β-strand	556-566	11	1
α-helix	569-583	15
α-helix	587	1
α-helix	590-592	3
β-strand	593-604	12	1

Chain B: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	476-489	14
β-strand	503-511	9	1
α-helix	514-527	14
β-strand	532-533	2	1
α-helix	534-536	3
β-strand	537-540	4	1
α-helix	541	1
α-helix	543-544	2
α-helix	549-552	4
β-strand	556-566	11	1
α-helix	569-583	15
α-helix	590-592	3
β-strand	593-604	12	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epstein-Barr nuclear antigen 1	A, B	protein	141	Epstein-Barr virus (strain B95-8)	P03211 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6NPI_1 Epstein-Barr nuclear antigen 1 (chains A, B)
SHMGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTAL
AIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTK
PAPTCNIRVTVCSFDDGVDLP

Ligands and cofactors

ID	Name	Formula	Copies
KW1	({2-[(4-bromo-5-methyl-1,2-oxazol-3-yl)amino]-2-oxoethyl}sulfanyl)acetic acid	C8 H9 Br N2 O4 S	1
60Q	2-pyrrol-1-ylbenzoic acid	C11 H9 N O2	1

Primary citation

Structure-based design of small-molecule inhibitors of EBNA1 DNA binding blocks Epstein-Barr virus latent infection and tumor growth. Messick, T.E., Smith, G.R., Soldan, S.S. et al. Sci Transl Med (2019) 11. DOI 10.1126/scitranslmed.aau5612 · PubMed

Other PDB entries of the same protein (UniProt P03211 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6VH6 1.3 Å, Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragment
6NPP 1.35 Å, Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments
2FYY 1.5 Å, The role of T cell receptor alpha genes in directing human MHC restriction
6NPM 1.6 Å, Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments
4PRE 1.65 Å, Crystal structure of a HLA-B*35:08-HPVG-Q5
1YY6 1.7 Å, The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with an EBNA1…
4PRA 1.85 Å, Crystal structure of a HLA-B*35:01-HPVG-Q5
2FZ3 1.9 Å, The role of T cell receptor alpha genes in directing human MHC restriction
5WMF 1.9 Å, Crystal structure of the Hexameric Ring of Epstein-Barr Virus Nuclear Antigen-1, EBNA1
3MV7 2.0 Å, Crystal Structure of the TK3 TCR in complex with HLA-B*3501/HPVG
5WUM 2.0 Å, Crystal structure of mouse importin-alpha1 bound to S385-phosphorylated NLS of EBNA1
3MV8 2.1 Å, Crystal Structure of the TK3-Gln55His TCR in complex with HLA-B*3501/HPVG

Browse structure collections

About this viewer

MolViewer shows 6NPI 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.