3C1B: Histone H3-like

The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure. Determined by X-ray diffraction at 2.2 Å resolution. Released 7 Oct 2008.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Xenopus laevis, Xenopus (Silurana) tropicalis
Chains: 10
Atoms: 12,828
Mol. weight: 199 kDa
Released: 7 Oct 2008

Explore 3C1B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3C1B contains 38 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	441-442	2
α-helix	445-456	12
α-helix	464-476	13
β-strand	483-484	2	1
α-helix	486-513	28
β-strand	518-519	2	2
α-helix	521-531	11

Chain B: 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	97-98	2	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	817-821	5
α-helix	827-836	10
β-strand	842-843	2	4
α-helix	846-872	27
β-strand	877-878	2	5
α-helix	880-888	9
α-helix	891-896	6
β-strand	900-902	3	6
α-helix	913-915	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1235-1245	11
β-strand	1250-1251	2	5
α-helix	1253-1280	28
β-strand	1285-1286	2	4
α-helix	1288-1298	11
α-helix	1301-1319	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	641-642	2
α-helix	645-656	12
α-helix	664-678	15
β-strand	683-684	2	7
α-helix	686-713	28
β-strand	718-719	2	8
α-helix	721-730	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	225-228	4
α-helix	231-240	10
β-strand	245-246	2	8
α-helix	250-275	26
β-strand	280-281	2	7
α-helix	283-292	10
β-strand	296-298	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1017-1021	5
α-helix	1027-1036	10
β-strand	1042-1043	2	9
α-helix	1046-1071	26
β-strand	1077-1078	2	10
α-helix	1080-1088	9
α-helix	1091-1096	6
β-strand	1101-1102	2	3
α-helix	1113-1115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1435-1445	11
β-strand	1450-1451	2	10
α-helix	1453-1480	28
β-strand	1485-1486	2	9
α-helix	1488-1498	11
α-helix	1501-1519	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3-like	A, E	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	C, G	protein	129	Xenopus laevis	P06897 (AlphaFold model)
Histone 2, H2bf	D, H	protein	125	Xenopus (Silurana) tropicalis	Q28D68 (AlphaFold model)
Palindromic 146bp Human Alpha satellite DNA	I, J	DNA	146

Sequence of entity 1 (A, E), FASTA

>3C1B_1 Histone H3-like (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>3C1B_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>3C1B_3 Histone H2A type 1 (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSTKSK

Sequence of entity 4 (D, H), FASTA

>3C1B_4 Histone 2, H2bf (chains D, H)
PDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK

Sequence of entity 5 (I, J), FASTA

>3C1B_5 Palindromic 146bp Human Alpha satellite DNA (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Primary citation

The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Lu, X., Simon, M.D., Chodaparambil, J.V. et al. Nat Struct Mol Biol (2008) 15:1122-1124. DOI 10.1038/nsmb.1489 · 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…
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
1P3I 2.3 Å, Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants

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