4KGC: Histone H3.2

Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM. Determined by X-ray diffraction at 2.69 Å resolution. Released 26 Mar 2014.

Method: X-ray diffraction
Resolution: 2.69 Å
Organisms: Xenopus laevis, synthetic construct
Chains: 10
Atoms: 12,091
Mol. weight: 200.93 kDa
Ligands: HRU, MG
Released: 26 Mar 2014

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

Secondary structure: helices and β-sheets

4KGC 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 A: 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 B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
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 C: 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	47-72	26
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chain D: 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	101-121	21

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
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 F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	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 G: 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

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	101-119	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	130	Xenopus laevis	Q6AZJ8 (AlphaFold model)
Histone H2B 1.1	D, H	protein	126	Xenopus laevis	P02281 (AlphaFold model)
DNA (145-mer)	I	DNA	145	synthetic construct
DNA (145-mer)	J	DNA	145	synthetic construct

Sequence of entity 1 (A, E), FASTA

>4KGC_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>4KGC_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>4KGC_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>4KGC_4 Histone H2B 1.1 (chains D, H)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (I), FASTA

>4KGC_5 DNA (145-mer) (chains I)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGTATCTGCAGGTGGATATTGAT

Sequence of entity 6 (J), FASTA

>4KGC_6 DNA (145-mer) (chains J)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGTATCTGCAGGTGGATATTGAT

Ligands and cofactors

ID	Name	Formula	Copies
HRU	chlorido(ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-…	C12 H22 Cl N2 Ru	4
MG	Magnesium ion	Mg	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity. Adhireksan, Z., Davey, G.E., Campomanes, P. et al. Nat Commun (2014) 5:3462-3462. DOI 10.1038/ncomms4462 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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