8Q3X: Histone H3.1

Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound). Determined by X-ray diffraction at 2.3 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, Human gammaherpesvirus 8
Chains: 11
Atoms: 12,178
Mol. weight: 179.18 kDa
Ligands: XIS, AU, MG
Released: 27 Mar 2024

Explore 8Q3X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q3X contains 39 α-helices and 20 β-strands across 8 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 AAA: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chain BBB: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain CCC: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chains DDD and HHH: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	101-119	19

Chain EEE: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-130	10

Chain FFF: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain GGG: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1	AAA, EEE	protein	98	Homo sapiens	P68431 (AlphaFold model)
Histone H4	BBB, FFF	protein	87	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	CCC, GGG	protein	107	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	DDD, HHH	protein	95	Homo sapiens	O60814 (AlphaFold model)
DNA (145-mer)	III	DNA	145	Homo sapiens
DNA (145-mer)	JJJ	DNA	145	Homo sapiens
LANA peptide	MMM	protein	14	Human gammaherpesvirus 8	Q9QR71

Sequence of entity 1 (AAA, EEE), FASTA

>8Q3X_1 Histone H3.1 (chains AAA, EEE)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (BBB, FFF), FASTA

>8Q3X_2 Histone H4 (chains BBB, FFF)
KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH
AKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (CCC, GGG), FASTA

>8Q3X_3 Histone H2A type 1-B/E (chains CCC, GGG)
KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARD
NKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK

Sequence of entity 4 (DDD, HHH), FASTA

>8Q3X_4 Histone H2B type 1-K (chains DDD, HHH)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 5 (III), FASTA

>8Q3X_5 DNA (145-MER) (chains III)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGTATCTGCAGGTGGATATTGAT

Sequence of entity 6 (JJJ), FASTA

>8Q3X_6 DNA (145-MER) (chains JJJ)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGTATCTGCAGGTGGATATTGAT

Sequence of entity 7 (MMM), FASTA

>8Q3X_7 LANA peptide (chains MMM)
PGARLRSGRSTGAP

Ligands and cofactors

ID	Name	Formula	Copies
XIS	4-diphenylphosphanylbenzoic acid	C19 H15 O2 P	1
AU	Gold ion	Au	1
MG	Magnesium ion	Mg	1

Primary citation

Viral peptide conjugates for metal-warhead delivery to chromatin. Batchelor, L.K., De Falco, L., Dyson, P.J. et al. RSC Adv (2024) 14:8718-8725. DOI 10.1039/d4ra01617c · PubMed

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

Browse structure collections

About this viewer

MolViewer shows 8Q3X 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.