9B3F: Yeast (Nap1)2-H2A-H2B-Kap114

Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114. Determined by electron microscopy at 3.54 Å resolution. Released 27 Nov 2024.

Method
Electron microscopy
Resolution
3.54 Å
Organism
Saccharomyces cerevisiae
Chains
5
Atoms
13,408
Mol. weight
214.6 kDa
Released
27 Nov 2024

Explore 9B3F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B3F contains 101 α-helices and 28 β-strands across 5 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: 58 helices, 6 β-strands

ElementResiduesLengthSheet
α-helix5-106
α-helix17-2812
α-helix31-4515
α-helix51-6515
α-helix84-9916
α-helix105-12117
α-helix128-14013
α-helix144-15613
α-helix160-1645
α-helix168-18114
α-helix187-20620
α-helix213-23523
α-helix243-26321
α-helix271-29020
α-helix303-32018
α-helix328-34215
α-helix344-3452
α-helix346-3549
α-helix356-3638
α-helix372-38110
α-helix385-40218
α-helix406-4083
α-helix409-42012
α-helix431-44717
α-helix453-46917
α-helix477-49418
α-helix498-51417
α-helix517-5215
α-helix523-54018
α-helix541-5433
α-helix546-56217
α-helix571-58717
α-helix592-60615
α-helix612-6143
α-helix616-6205
α-helix622-63413
α-helix641-65616
α-helix662-6643
α-helix665-68117
α-helix685-70117
α-helix704-7074
α-helix708-7103
α-helix711-72212
α-helix728-7325
α-helix734-74411
α-helix750-76617
α-helix770-78617
α-helix788-79710
β-strand799-80028
β-strand803-80428
α-helix805-81713
α-helix823-83917
α-helix842-8465
β-strand848-84929
β-strand853-854210
α-helix855-8562
α-helix864-8674
β-strand873-874210
β-strand877-87829
α-helix879-89416
α-helix933-9419
α-helix965-97915
α-helix981-99010
α-helix993-100311
Chain B: 5 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix18-225
α-helix28-3811
β-strand44111
α-helix47-7327
β-strand78-79212
α-helix81-9010
α-helix92-987
Chain C: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix41-5111
β-strand56-57212
α-helix59-8628
β-strand92111
α-helix94-10411
α-helix107-12519
Chain D: 17 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix82-876
α-helix90-14051
α-helix147-15812
α-helix163-1653
α-helix167-1682
α-helix169-1724
α-helix176-1794
α-helix188-1947
α-helix197-2004
α-helix205-2117
β-strand216-22161
β-strand228-23471
β-strand24312
β-strand247-25481
β-strand266-27161
β-strand27612
β-strand285-294103
β-strand299-308103
α-helix312-3154
α-helix323-33311
α-helix334-3385
α-helix339-3479
α-helix348-3525
α-helix353-3553
α-helix356-3616
Chain E: 17 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix84-874
α-helix90-14051
α-helix147-16014
α-helix163-1653
α-helix169-1724
α-helix176-1794
α-helix1851
α-helix188-1958
α-helix199-2024
α-helix205-2117
β-strand214-22294
β-strand228-23584
β-strand24315
β-strand247-25484
β-strand25916
α-helix260-2623
β-strand26316
α-helix264-2652
β-strand266-27164
β-strand27615
β-strand285-29397
β-strand300-30897
α-helix312-3154
α-helix325-3273
α-helix328-34720
α-helix348-3525
α-helix357-3615

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
NAP1 isoform 1D, Eprotein313Saccharomyces cerevisiaeP25293 (AlphaFold model)
KAP114 isoform 1Aprotein1007Saccharomyces cerevisiaeP53067 (AlphaFold model)
Histone H2ABprotein131Saccharomyces cerevisiaeP04912 (AlphaFold model)
Histone H2BCprotein130Saccharomyces cerevisiaeP02294 (AlphaFold model)
Sequence of entity 1 (D, E), FASTA
>9B3F_1 NAP1 isoform 1 (chains D, E)
MGSSHHHHHHSSGLVPRGSHMLGSLVGQDSGYVGGLPKNVKEKLLSLKTLQSELFEVEKE
FQVEMFELENKFLQKYKPIWEQRSRIISGQEQPKPEQIAKGQEIVESLNETELLVDEEEK
AQNDSEEEQVKGIPSFWLTALENLPIVCDTITDRDAEVLEYLQDIGLEYLTDGRPGFKLL
FRFDSSANPFFTNDILCKTYFYQKELGYSGDFIYDHAEGCEISWKDNAHNVTVDLEMRKQ
RNKTTKQVRTIEKITPIESFFNFFDPPKIQNEDQDEELEEDLEERLALDYSIGEQLKDKL
IPRAVDWFTGAAL
Sequence of entity 2 (A), FASTA
>9B3F_2 KAP114 isoform 1 (chains A)
GGSMDINELIIGAQSADKHTREVAETQLLQWCDSDASQVFKALANVALQHEASLESRQFA
LLSLRKLITMYWSPGFESYRSTSNVEIDVKDFIREVLLKLCLNDNENTKIKNGASYCIVQ
ISAVDFPDQWPQLLTVIYDAISHQHSLNAMSLLNEIYDDVVSEEMFFEGGIGLATMEIVF
KVLNTETSTLIAKIAALKLLKACLLQMSSHNEYDEASRKSFVSQCLATSLQILGQLLTLN
FGNVDVISQLKFKSIIYENLVFIKNDFSRKHFSSELQKQFKIMAIQDLENVTHINANVET
TESEPLLETVHDCSIYIVEFLTSVCTLQFSVEEMNKIITSLTILCQLSSETREIWTSDFN
TFVSKETGLAASYNVRDQANEFFTSLPNPQLSLIFKVVSNDIEHSTCNYSTLESLLYLLQ
CILLNDDEITGENIDQSLQILIKTLENILVSQEIPELILARAILTIPRVLDKFIDALPDI
KPLTSAFLAKSLNLALKSDKELIKSATLIAFTYYCYFAELDSVLGPEVCSETQEKVIRII
NQVSSDAEEDTNGALMEVLSQVISYNPKEPHSRKEILQAEFHLVFTISSEDPANVQVVVQ
SQECLEKLLDNINMDNYKNYIELCLPSFINVLDSNNANNYRYSPLLSLVLEFITVFLKKK
PNDGFLPDEINQYLFEPLAKVLAFSTEDETLQLATEAFSYLIFNTDTRAMEPRLMDIMKV
LERLLSLEVSDSAAMNVGPLVVAIFTRFSKEIQPLIGRILEAVVVRLIKTQNISTEQNLL
SVLCFLTCNDPKQTVDFLSSFQIDNTDALTLVMRKWIEAFEVIRGEKRIKENIVALSNLF
FLNDKRLQKVVVNGNLIPYEGDLIITRSMAKKMPDRYVQVPLYTKIIKLFVSELSFQSKQ
PNPEQLITSDIKQEVVNANKDDDNDDWEDVDDVLDYDKLKEYIDDDVDEEADDDSDDITG
LMDVKESVVQLLVRFFKEVASKDVSGFHCIYETLSDSERKVLSEALL
Sequence of entity 3 (B), FASTA
>9B3F_3 Histone H2A (chains B)
SGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLA
AEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKK
SAKTAKASQEL
Sequence of entity 4 (C), FASTA
>9B3F_4 Histone H2B (chains C)
SSAAEKKPASKAPAEKKPAAKKTSTSVDGKKRSKVRKETYSSYIYKVLKQTHPDTGISQK
SMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRA
VTKYSSSTQA

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:

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