6HAU: KSHV PAN RNA Mta-response element fragment

KSHV PAN RNA Mta-response element fragment complexed with the globular domain of herpesvirus saimiri ORF57. Determined by X-ray diffraction at 1.86 Å resolution. Released 21 Nov 2018.

Method: X-ray diffraction
Resolution: 1.86 Å
Organisms: Saimiriine herpesvirus 2 (strain 11), Human herpesvirus 8
Chains: 3
Atoms: 5,002
Mol. weight: 67.05 kDa
Ligands: ZN
Released: 21 Nov 2018

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

Secondary structure: helices and β-sheets

6HAU contains 41 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: 21 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	146-149	4
β-strand	151	1	1
α-helix	153-155	3
α-helix	157-158	2
α-helix	162-163	2
α-helix	169-177	9
α-helix	182-191	10
α-helix	197-200	4
β-strand	201-203	3	2
α-helix	207-218	12
α-helix	224-236	13
α-helix	240-259	20
α-helix	262-264	3
α-helix	273-275	3
α-helix	276-289	14
α-helix	293-296	4
α-helix	303-316	14
α-helix	319-326	8
β-strand	331	1	3
α-helix	334-350	17
α-helix	353-355	3
α-helix	356-368	13
α-helix	373-388	16
α-helix	392-402	11
β-strand	414-416	3	2

Chain B: 20 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	146-149	4
β-strand	151	1	3
α-helix	153-155	3
α-helix	172-177	6
α-helix	182-191	10
α-helix	197-200	4
β-strand	201-203	3	4
α-helix	204-206	3
α-helix	208-218	11
α-helix	224-236	13
α-helix	240-259	20
α-helix	262-264	3
α-helix	273-275	3
α-helix	276-289	14
α-helix	293-296	4
α-helix	303-316	14
α-helix	319-326	8
β-strand	331	1	1
α-helix	334-350	17
α-helix	353-355	3
α-helix	356-368	13
α-helix	373-386	14
α-helix	394-402	9
β-strand	414-416	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mRNA export factor ICP27 homolog	A, B	protein	273	Saimiriine herpesvirus 2 (strain 11)	P13199 (AlphaFold model)
MRE fragment of PAN RNA	D	RNA	17	Human herpesvirus 8

Sequence of entity 1 (A, B), FASTA

>6HAU_1 mRNA export factor ICP27 homolog (chains A, B)
GPLLKLFDISILPKSGEPKLFLPVPSLPCQEAEKTNDKYVLAMAQRAMHDVPISSKQLTA
NLLPVKFKPLLSIVRYTPNYYYWVSMRKETIASANLCTVAAFLDESLCWGQQYLKNDFIF
SENGKDIILDTSSALLSQLVHKIKMLPFCHCLMQTTPQDHIVKQVCYLIASNNRILDAVR
YLQTSVIKSPIVLLLAYAVCLPAAIICTKNETQLYSHCMRILKEYRPGDVMNILHESLTQ
HLNKCPSSTCAYTTRAIVGTKANTTGLFFLPTQ

Sequence of entity 2 (D), FASTA

>6HAU_2 MRE fragment of PAN RNA (chains D)
CACCUAUGGAUUUUGUG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (ACT) are not listed.

Primary citation

Structural identification of conserved RNA binding sites in herpesvirus ORF57 homologs: implications for PAN RNA recognition. Tunnicliffe, R.B., Levy, C., Ruiz Nivia, H.D. et al. Nucleic Acids Res (2019) 47:1987-2001. DOI 10.1093/nar/gky1181 · PubMed

Other PDB entries of the same protein (UniProt P13199 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HAT 1.86 Å, Globular domain of herpesvirus saimiri ORF57
2YKA RRM domain of mRNA export adaptor REF2-I bound to HVS ORF57 peptide

Browse structure collections

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