7V1M: The co-chaperone relationship of sNASP and ASF1b

Name: PDB 7V1M: Structural basis for the co-chaperone relationship of sNASP and ASF1b
Published: 2022-04-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Structural basis for the co-chaperone relationship of sNASP and ASF1b. Determined by X-ray diffraction at 2.83 Å resolution. Released 20 Apr 2022.

Method: X-ray diffraction
Resolution: 2.83 Å
Organism: Homo sapiens
Chains: 8
Atoms: 7,966
Mol. weight: 141.97 kDa
Released: 20 Apr 2022

Explore 7V1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V1M contains 45 α-helices and 33 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: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	65-78	14
α-helix	86-113	28
β-strand	118-119	2	6
α-helix	121-131	11

Chain B: 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 C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
α-helix	31-39	9
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 D: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	4
β-strand	16-17	2	3
α-helix	21	1
β-strand	22-30	9	4
β-strand	34	1	5
β-strand	38-45	8	3
α-helix	51-53	3
β-strand	54-62	9	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

Chain E: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-41	11
β-strand	45-46	2	6
α-helix	50-74	25
α-helix	83-91	9
β-strand	95-97	3	7

Chain F: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	8
β-strand	16-17	2	7
α-helix	21	1
β-strand	22-30	9	8
β-strand	34	1	9
β-strand	38-44	7	7
β-strand	47	1	10
β-strand	50	1	10
α-helix	51-53	3
β-strand	55-62	8	7
β-strand	65	1	9
β-strand	68-76	9	8
α-helix	81-83	3
α-helix	86-89	4
β-strand	91-101	11	7
β-strand	104-117	14	7
α-helix	120-124	5
β-strand	135-148	14	7

Chain G: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	41-56	16
α-helix	59-76	18
α-helix	82-84	3
α-helix	85-99	15
α-helix	175-192	18
α-helix	196-215	20
α-helix	219-234	16
α-helix	242-257	16
α-helix	261-281	21
α-helix	299-317	19

Chain H: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	39-56	18
α-helix	59-77	19
α-helix	82-84	3
α-helix	85-98	14
α-helix	172-192	21
α-helix	196-215	20
α-helix	219-236	18
α-helix	242-257	16
α-helix	261-281	21
α-helix	300-317	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3	A, B	protein	135	Homo sapiens	P84243 (AlphaFold model)
Histone H4	C, E	protein	102	Homo sapiens	P62805 (AlphaFold model)
Histone chaperone ASF1B	D, F	protein	158	Homo sapiens	Q9NVP2 (AlphaFold model)
Isoform 2 of Nuclear autoantigenic sperm protein	G, H	protein	235	Homo sapiens	P49321 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7V1M_1 Histone H3.3 (chains A, B)
ARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (C, E), FASTA

>7V1M_2 Histone H4 (chains C, E)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (D, F), FASTA

>7V1M_3 Histone chaperone ASF1B (chains D, F)
MAKVSVLNVAVLENPSPFHSPFRFEISFECSEALADDLEWKIIYVGSAESEEFDQILDSV
LVGPVPAGRHMFVFQADAPNPSLIPETDAVGVTVVLITCTYHGQEFIRVGYYVNNEYLNP
ELRENPPMKPDFSQLQRNILASNPRVTRFHINWDNNMD

Sequence of entity 4 (G, H), FASTA

>7V1M_4 Isoform 2 of Nuclear autoantigenic sperm protein (chains G, H)
SADKVESLDVDSEAKKLLGLGQKHLVMGDIPAAVNAFQEAASLLGKKYGETANECGEAFF
FYGKSLLELARLENKSLQENEEEEIGNLELAWDMLDLAKIIFKRQETKEAQLYAAQAHLK
LGEVSVESENYVQAVEEFQSCLNLQEQYLEAHDRLLAETHYQLGLAYGYNSQYDEAVAQF
SKSIEVIENRMAVLNEQVKEAEGSSAEYKKEIEELKELLPEIREKIEDAKESQRS

Primary citation

NASP maintains histone H3-H4 homeostasis through two distinct H3 binding modes. Bao, H., Carraro, M., Flury, V. et al. Nucleic Acids Res (2022) 50:5349-5368. DOI 10.1093/nar/gkac303 · 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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