5T7X: HHV-4 EBNA1 DNA binding domain

Crystal structure of HHV-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA. Determined by X-ray diffraction at 2.35 Å resolution. Released 19 Jul 2017.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Human herpesvirus 4 (strain B95-8)
Chains: 4
Atoms: 3,126
Mol. weight: 43.7 kDa
Released: 19 Jul 2017

Explore 5T7X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T7X contains 18 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: 9 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	543-545	3
α-helix	549-552	4
β-strand	556-566	11	1
α-helix	569-584	16
α-helix	587	1
α-helix	590-592	3
β-strand	593-604	12	1

Chain B: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	476-491	16
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	569-584	16
α-helix	587	1
α-helix	590-592	3
β-strand	593-604	12	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(gpgpaptpapgpcpcptpaptpgpcptpapcpcpc)-3')	C	DNA	18	Human herpesvirus 4 (strain B95-8)
DNA (5'-d(gpgpgptpapgpcpaptpapgpgpcptpaptpcpc)-3')	D	DNA	18	Human herpesvirus 4 (strain B95-8)
Epstein-Barr nuclear antigen 1	A, B	protein	149	Human herpesvirus 4 (strain B95-8)	P03211 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>5T7X_1 DNA (5'-D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3') (chains C)
GGATAGCCTATGCTACCC

Sequence of entity 2 (D), FASTA

>5T7X_2 DNA (5'-D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3') (chains D)
GGGTAGCATAGGCTATCC

Sequence of entity 3 (A, B), FASTA

>5T7X_3 Epstein-Barr nuclear antigen 1 (chains A, B)
RKKGGWFGKHRGQGGSNPKFENIAEGLRVLLARSHVERTTEEGNWVAGVFVYGGSKTSLY
NLRRGIALAVPQCRITPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDA
IKDLVMIKPAPTCNIKVTVCSFDDGVDLP

Primary citation

Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency. Dheekollu, J., Malecka, K., Wiedmer, A. et al. Oncotarget (2017) 8:7248-7264. DOI 10.18632/oncotarget.14540 · 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
6NPI 1.5 Å, Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments
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

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