4HLY: PDB entry 4HLY

The complex crystal structure of the DNA binding domain of vIRF-1 from the oncogenic KSHV with DNA. Determined by X-ray diffraction at 1.48 Å resolution. Released 13 Mar 2013.

Method: X-ray diffraction
Resolution: 1.48 Å
Organisms: Human herpesvirus 8, synthetic construct
Chains: 4
Atoms: 2,497
Mol. weight: 38 kDa
Released: 13 Mar 2013

Explore 4HLY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HLY contains 10 α-helices and 8 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: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
β-strand	23-24	2	1
β-strand	31-35	5	1
α-helix	46-50	5
α-helix	51-59	9
α-helix	67-69	3
α-helix	73-83	11
β-strand	88-95	8	1
β-strand	101-107	7	1

Chain B: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
β-strand	23-24	2	2
β-strand	31-35	5	2
α-helix	46-49	4
α-helix	51-60	10
α-helix	67-69	3
α-helix	73-84	12
β-strand	88-95	8	2
β-strand	101-107	7	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
K9	A, B	protein	132	Human herpesvirus 8	F5HF68 (AlphaFold model)
5'-d(gpcpgptpcpgpapgpapcpgpc)-3'	C, D	DNA	12	synthetic construct

Sequence of entity 1 (A, B), FASTA

>4HLY_1 K9 (chains A, B)
MHHHHHHSSGVDLGTENLYFQSMGKASIKDWIVCQVNSGKFPGVEWEDEERTRFRIPVTP
LADPCFEWRRDGELGVVYIRERGNMPVDASFKGTRGRRRMLAALRRTRGLQEIGKGISQD
GHHFLVFRVRKP

Sequence of entity 2 (C, D), FASTA

>4HLY_2 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3' (chains C, D)
GCGTCGAGACGC

Primary citation

The crystal structure of the DNA-binding domain of vIRF-1 from the oncogenic KSHV reveals a conserved fold for DNA binding and reinforces its role as a transcription factor. Hew, K., Dahlroth, S.L., Venkatachalam, R. et al. Nucleic Acids Res (2013) 41:4295-4306. DOI 10.1093/nar/gkt082 · PubMed

Other PDB entries of the same protein (UniProt F5HF68 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YSI 1.02 Å, Structure of USP7 with a novel viral protein

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