7CJ0: DNAJC9 HBD

Name: PDB 7CJ0: Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD
Published: 2021-04-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD. Determined by X-ray diffraction at 2.5 Å resolution. Released 14 Apr 2021.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 8
Atoms: 4,696
Mol. weight: 75.3 kDa
Released: 14 Apr 2021

Explore 7CJ0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CJ0 contains 25 α-helices and 13 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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	173-204	32
α-helix	213-242	30

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	64-76	13
β-strand	83	1	3
β-strand	84-85	2	4
α-helix	86-113	28
β-strand	118-119	2	5
α-helix	121-131	11

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	5
α-helix	50-75	26
β-strand	80	1	3
α-helix	83-96	14

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	175-207	33
α-helix	209-210	2
α-helix	213-242	30
α-helix	244-247	4

Chain E: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain F: 4 helices, 2 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	83-96	14

Chain G: 3 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	103-106	4
α-helix	107-122	16

Chain H: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	70-71	2	5
β-strand	95-96	2	4
α-helix	103-106	4
α-helix	107-124	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3	B, E	protein	79	Homo sapiens	P84243 (AlphaFold model)
Histone H4	C, F	protein	102	Homo sapiens	P62805 (AlphaFold model)
DNA replication licensing factor MCM2	G, H	protein	70	Homo sapiens	P49736 (AlphaFold model)
DnaJ homolog subfamily C member 9	A, D	protein	84	Homo sapiens	Q8WXX5 (AlphaFold model)

Sequence of entity 1 (B, E), FASTA

>7CJ0_1 Histone H3.3 (chains B, E)
STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA

Sequence of entity 2 (C, F), FASTA

>7CJ0_2 Histone H4 (chains C, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (G, H), FASTA

>7CJ0_3 DNA replication licensing factor MCM2 (chains G, H)
GPLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQR
DREAGRGLGR

Sequence of entity 4 (A, D), FASTA

>7CJ0_4 DnaJ homolog subfamily C member 9 (chains A, D)
GPLGSEVPSYNAFVKESKQKMNARKRRAQEEAKEAEMSRKELGLDEGVDSLKAAIQSRQK
DRQKEMDNFLAQMEAKYSKSSKGG

Primary citation

DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network. Hammond, C.M., Bao, H., Hendriks, I.A. et al. Mol Cell (2021) 81:2533-2548.e9. DOI 10.1016/j.molcel.2021.03.041 · 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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