5BO0: Histone H3.2

Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.2-H4 dimer. Determined by X-ray diffraction at 2.91 Å resolution. Released 17 Jun 2015.

Method: X-ray diffraction
Resolution: 2.91 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,970
Mol. weight: 46.36 kDa
Released: 17 Jun 2015

Explore 5BO0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5BO0 contains 16 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: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-78	15
β-strand	83-84	2	1
α-helix	86-112	27
β-strand	119	1	2
α-helix	121-130	10

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	21-23	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	83-91	9
β-strand	95-97	3	3

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	70-71	2	2
α-helix	77-81	5
β-strand	95	1	1
α-helix	108-120	13

Chain D: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	4
β-strand	16-17	2	3
α-helix	21	1
β-strand	22-30	9	4
β-strand	34	1	5
β-strand	38-44	7	3
α-helix	51-53	3
β-strand	55-62	8	3
β-strand	65	1	5
β-strand	68-76	9	4
α-helix	77-79	3
α-helix	81-83	3
α-helix	86-89	4
β-strand	91-101	11	3
β-strand	104-117	14	3
α-helix	120-124	5
α-helix	132-134	3
β-strand	135-139	5	3
β-strand	145-148	4	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A	protein	80	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	B	protein	102	Homo sapiens	P62805 (AlphaFold model)
DNA replication licensing factor MCM2	C	protein	70	Homo sapiens	P49736 (AlphaFold model)
Histone chaperone ASF1B	D	protein	158	Homo sapiens	Q9NVP2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5BO0_1 Histone H3.2 (chains A)
KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAK
RVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B), FASTA

>5BO0_2 Histone H4 (chains B)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C), FASTA

>5BO0_3 DNA replication licensing factor MCM2 (chains C)
GPLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQR
DREAGRGLGR

Sequence of entity 4 (D), FASTA

>5BO0_4 Histone chaperone ASF1B (chains D)
MAKVSVLNVAVLENPSPFHSPFRFEISFECSEALADDLEWKIIYVGSAESEEFDQILDSV
LVGPVPAGRHMFVFQADAPNPSLIPETDAVGVTVVLITCTYHGQEFIRVGYYVNNEYLNP
ELRENPPMKPDFSQLQRNILASNPRVTRFHINWDNNMD

Primary citation

A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks. Huang, H., Strmme, C.B., Saredi, G. et al. Nat Struct Mol Biol (2015) 22:618-626. DOI 10.1038/nsmb.3055 · PubMed

Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

Browse structure collections

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