9B23: Nap1 core

Name: PDB 9B23: Cryo-EM structure of Nap1 core
Published: 2024-11-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Cryo-EM structure of Nap1 core. Determined by electron microscopy at 3.2 Å resolution. Released 27 Nov 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 4,670
Mol. weight: 72.36 kDa
Released: 27 Nov 2024

Explore 9B23 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B23 contains 34 α-helices and 18 β-strands across 2 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 D: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	82-87	6
α-helix	90-140	51
α-helix	147-158	12
α-helix	163-165	3
α-helix	167-168	2
α-helix	169-172	4
α-helix	176-179	4
α-helix	188-195	8
α-helix	197-200	4
α-helix	205-211	7
β-strand	216-221	6	1
β-strand	228-234	7	1
β-strand	243	1	2
β-strand	247-254	8	1
β-strand	266-271	6	1
α-helix	272-274	3
β-strand	276	1	2
β-strand	285-294	10	3
β-strand	299-308	10	3
α-helix	312-315	4
α-helix	323-325	3
α-helix	326-330	5
α-helix	331-347	17
α-helix	348-352	5
α-helix	353-355	3
α-helix	356-361	6

Chain E: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	84-87	4
α-helix	90-140	51
α-helix	147-160	14
α-helix	163-165	3
α-helix	169-172	4
α-helix	176-179	4
α-helix	185	1
α-helix	188-195	8
α-helix	199-202	4
α-helix	205-211	7
β-strand	214-222	9	4
β-strand	228-235	8	4
β-strand	243	1	5
β-strand	247-254	8	4
β-strand	259	1	6
α-helix	260-262	3
β-strand	263	1	6
β-strand	266-271	6	4
β-strand	276	1	5
β-strand	285-293	9	7
β-strand	300-308	9	7
α-helix	312-315	4
α-helix	325-327	3
α-helix	328-347	20
α-helix	348-352	5
α-helix	357-361	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAP1 isoform 1	D, E	protein	313	Saccharomyces cerevisiae	P25293 (AlphaFold model)

Sequence of entity 1 (D, E), FASTA

>9B23_1 NAP1 isoform 1 (chains D, E)
MGSSHHHHHHSSGLVPRGSHMLGSLVGQDSGYVGGLPKNVKEKLLSLKTLQSELFEVEKE
FQVEMFELENKFLQKYKPIWEQRSRIISGQEQPKPEQIAKGQEIVESLNETELLVDEEEK
AQNDSEEEQVKGIPSFWLTALENLPIVCDTITDRDAEVLEYLQDIGLEYLTDGRPGFKLL
FRFDSSANPFFTNDILCKTYFYQKELGYSGDFIYDHAEGCEISWKDNAHNVTVDLEMRKQ
RNKTTKQVRTIEKITPIESFFNFFDPPKIQNEDQDEELEEDLEERLALDYSIGEQLKDKL
IPRAVDWFTGAAL

Primary citation

Nap1 and Kap114 co-chaperone H2A-H2B and facilitate targeted histone release in the nucleus. Fung, H.Y.J., Jiou, J., Niesman, A.B. et al. J Cell Biol (2025) 224. DOI 10.1083/jcb.202408193 · PubMed

Other PDB entries of the same protein (UniProt P25293 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9B3I 2.88 Å, Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114-RanGTP
2AYU 3.0 Å, The structure of nucleosome assembly protein suggests a mechanism for histone binding…
2Z2R 3.2 Å, Nucleosome assembly proteins I (NAP-1, 74-365)
9B31 3.2 Å, Cryo-EM structure of yeast (Nap1)2-Kap114-H2A-H2B
9B3F 3.54 Å, Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114
5G2E 6.7 Å, Structure of the Nap1 H2A H2B complex

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