5KDM: EBV tegument protein BNRF1

Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4. Determined by X-ray diffraction at 3.5 Å resolution. Released 7 Sept 2016.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Homo sapiens, Epstein-Barr virus (strain AG876)
Chains: 4
Atoms: 4,341
Mol. weight: 74.63 kDa
Released: 7 Sept 2016

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

Secondary structure: helices and β-sheets

5KDM contains 25 α-helices and 19 β-strands across 4 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	48-57	10
α-helix	64-78	15
β-strand	83-85	3	1
α-helix	86-109	24
β-strand	119	1	2
α-helix	121-130	10

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	46	1	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-90	8
α-helix	95-97	3
β-strand	100	1	3

Chain C: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	185-207	23
β-strand	209-210	2	1
α-helix	212-216	5
α-helix	221-242	22
α-helix	267-272	6
α-helix	286-298	13
α-helix	306-334	29
α-helix	339-342	4
α-helix	350-352	3
α-helix	355-383	29

Chain D: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	393-397	5	4
α-helix	415-433	19
β-strand	439	1	4
β-strand	443	1	4
β-strand	450	1	5
α-helix	451-456	6
β-strand	463-467	5	4
α-helix	473-476	4
α-helix	491-500	10
α-helix	503	1
β-strand	504	1	5
α-helix	505	1
β-strand	508-512	5	4
β-strand	519	1	6
β-strand	522	1	6
α-helix	524-534	11
β-strand	539-546	8	4
β-strand	548	1	3
β-strand	551-554	4	4
α-helix	560-562	3
β-strand	575-576	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3	A	protein	135	Homo sapiens	P84243 (AlphaFold model)
Histone H4	B	protein	102	Homo sapiens	P62805 (AlphaFold model)
Death domain-associated protein 6	C	protein	212	Homo sapiens	Q9UER7 (AlphaFold model)
Major tegument protein	D	protein	219	Epstein-Barr virus (strain AG876)	Q1HVJ0

Sequence of entity 1 (A), FASTA

>5KDM_1 Histone H3.3 (chains A)
ARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B), FASTA

>5KDM_2 Histone H4 (chains B)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C), FASTA

>5KDM_3 Death domain-associated protein 6 (chains C)
SPRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSAYLQEARLKRKLIRLFG
RLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGPDTFPDYGDVLRAVEKAA
ARHSLGLPRQQLQLMAQDAFRDVGIRLQERRHLDLIYNFGCHLTDDYRPGVDPALSDPVL
ARRLRENRSLAMSRLDEVISKYAMLQDKSEEG

Sequence of entity 4 (D), FASTA

>5KDM_4 Major tegument protein (chains D)
QALDTVRYDYGHYLIMLGPFQPWSGLTAPPCPYAESSWAQAAVQTALELFSALYPAPCIS
GYARPPGPSAVIEHLGSLVPKGGLLLFLSHLPDDVKDGLGEMGPARATGPGMQQFVSSYF
LNPACSNVFITVRQRGEKINGRTVLQALGRACDMAGCQHYVLGSTVPLGGLNFVNDLASP
VSTAEMMDDFSPFFTVEFPPIQEEGASSPVPLDVDESMD

Primary citation

Structural basis underlying viral hijacking of a histone chaperone complex. Huang, H., Deng, Z., Vladimirova, O. et al. Nat Commun (2016) 7:12707-12707. DOI 10.1038/ncomms12707 · PubMed

Other PDB entries of the same protein (UniProt P84243 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3QL9 0.93 Å, Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide
4GNE 1.47 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7
4L58 1.48 Å, Crystal structure of the MLL5 PHD finger in complex with H3K4me3
5JLB 1.5 Å, Crystal structure of SETD2 bound to histone H3.3 K36I peptide
4GNF 1.55 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15
3QLA 1.6 Å, Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide
3MUL 1.65 Å, Crystal structure of Brd4 bromodomain 1 with butyrylated histone H3-K(buty)14
9G4A 1.65 Å, Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
4GNG 1.73 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide
3MUK 1.75 Å, Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23
4QQ4 1.75 Å, CW-type zinc finger of MORC3 in complex with the amino terminus of histone H3
1PDQ 1.76 Å, Polycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27.

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