5BNV: Histone H3.3

Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer. Determined by X-ray diffraction at 2.79 Å resolution. Released 17 Jun 2015.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,313
Mol. weight: 56.59 kDa
Ligands: PO4
Released: 17 Jun 2015

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

Secondary structure: helices and β-sheets

5BNV contains 18 α-helices and 12 β-strands across 6 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	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-25	5
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

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	70-71	2	2
α-helix	77-81	5
α-helix	85-87	3
β-strand	95	1	1
α-helix	107-122	16

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-78	15
β-strand	83-84	2	3
α-helix	86-113	28
β-strand	119	1	4
α-helix	121-130	10

Chain E: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	4
α-helix	50-76	27
β-strand	80-81	2	3
α-helix	83-91	9

Chain F: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	70-71	2	4
α-helix	77-81	5
β-strand	95	1	3
α-helix	107-122	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3	A, D	protein	79	Homo sapiens	P84243 (AlphaFold model)
Histone H4	B, E	protein	102	Homo sapiens	P62805 (AlphaFold model)
DNA replication licensing factor MCM2	C, F	protein	70	Homo sapiens	P49736 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5BNV_1 Histone H3.3 (chains A, D)
STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, E), FASTA

>5BNV_2 Histone H4 (chains B, E)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, F), FASTA

>5BNV_3 DNA replication licensing factor MCM2 (chains C, F)
GPLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQR
DREAGRGLGR

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3

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 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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