9B31: Yeast (Nap1)2-Kap114-H2A-H2B

Cryo-EM structure of yeast (Nap1)2-Kap114-H2A-H2B. Determined by electron microscopy at 3.2 Å resolution. Released 27 Nov 2024.

Method
Electron microscopy
Resolution
3.2 Å
Organism
Saccharomyces cerevisiae
Chains
5
Atoms
13,529
Mol. weight
214.8 kDa
Released
27 Nov 2024

Explore 9B31 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B31 contains 98 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: 56 helices, 4 β-strands

ElementResiduesLengthSheet
α-helix3-119
α-helix15-3117
α-helix33-4614
α-helix51-6818
α-helix84-9916
α-helix105-12218
α-helix130-1367
α-helix137-1415
α-helix144-15714
α-helix1601
α-helix161-1655
α-helix168-18114
α-helix187-20519
α-helix213-23422
α-helix243-26321
α-helix271-29121
α-helix303-32018
α-helix328-34114
α-helix344-3452
α-helix346-3549
α-helix356-3638
α-helix372-38211
α-helix385-40117
α-helix406-42015
α-helix425-4262
α-helix431-44717
α-helix453-46917
α-helix477-49216
α-helix498-51417
α-helix517-54125
α-helix546-56116
α-helix571-58717
α-helix592-60514
α-helix611-63424
α-helix641-65515
α-helix663-6642
α-helix665-68117
α-helix685-70117
α-helix704-7074
α-helix708-7103
α-helix711-72212
α-helix734-74411
α-helix746-7494
α-helix750-7523
α-helix753-76614
α-helix770-78617
α-helix788-79710
β-strand799-80021
β-strand803-80421
α-helix805-81713
α-helix823-83917
α-helix842-8454
β-strand848-85362
α-helix864-8674
β-strand874-87852
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-helix28-3710
β-strand43-4423
α-helix47-7327
β-strand78-7924
α-helix81-899
α-helix92-987
Chain C: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix38-5114
β-strand56-5724
α-helix59-8628
β-strand91-9223
α-helix94-10411
α-helix107-12317
Chain D: 16 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix82-876
α-helix90-14051
α-helix147-15812
α-helix163-1653
α-helix167-1682
α-helix169-1735
α-helix176-1794
α-helix188-1958
α-helix197-2004
α-helix205-2117
β-strand216-22165
β-strand228-23475
β-strand24316
β-strand247-258125
β-strand264-27185
β-strand27616
β-strand285-29177
β-strand29418
β-strand29918
β-strand302-30877
α-helix312-3154
α-helix323-3286
α-helix330-34718
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-helix188-1947
α-helix199-2024
α-helix205-2117
β-strand214-22299
β-strand228-23589
β-strand243110
β-strand247-25489
α-helix2581
β-strand259111
α-helix260-2623
β-strand263111
α-helix264-2652
β-strand266-27169
β-strand276110
β-strand285-293912
β-strand300-308912
α-helix312-3154
α-helix325-3273
α-helix328-34720
α-helix348-3525
α-helix357-3615

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
KAP114 isoform 1Aprotein1010Saccharomyces cerevisiaeP53067 (AlphaFold model)
Histone H2ABprotein131Saccharomyces cerevisiaeP04912 (AlphaFold model)
Histone H2BCprotein130Saccharomyces cerevisiaeP02294 (AlphaFold model)
NAP1 isoform 1D, Eprotein313Saccharomyces cerevisiaeP25293 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9B31_1 KAP114 isoform 1 (chains A)
GGSGGSMDINELIIGAQSADKHTREVAETQLLQWCDSDASQVFKALANVALQHEASLESR
QFALLSLRKLITMYWSPGFESYRSTSNVEIDVKDFIREVLLKLCLNDNENTKIKNGASYC
IVQISAVDFPDQWPQLLTVIYDAISHQHSLNAMSLLNEIYDDVVSEEMFFEGGIGLATME
IVFKVLNTETSTLIAKIAALKLLKACLLQMSSHNEYDEASRKSFVSQCLATSLQILGQLL
TLNFGNVDVISQLKFKSIIYENLVFIKNDFSRKHFSSELQKQFKIMAIQDLENVTHINAN
VETTESEPLLETVHDCSIYIVEFLTSVCTLQFSVEEMNKIITSLTILCQLSSETREIWTS
DFNTFVSKETGLAASYNVRDQANEFFTSLPNPQLSLIFKVVSNDIEHSTCNYSTLESLLY
LLQCILLNDDEITGENIDQSLQILIKTLENILVSQEIPELILARAILTIPRVLDKFIDAL
PDIKPLTSAFLAKSLNLALKSDKELIKSATLIAFTYYCYFAELDSVLGPEVCSETQEKVI
RIINQVSSDAEEDTNGALMEVLSQVISYNPKEPHSRKEILQAEFHLVFTISSEDPANVQV
VVQSQECLEKLLDNINMDNYKNYIELCLPSFINVLDSNNANNYRYSPLLSLVLEFITVFL
KKKPNDGFLPDEINQYLFEPLAKVLAFSTEDETLQLATEAFSYLIFNTDTRAMEPRLMDI
MKVLERLLSLEVSDSAAMNVGPLVVAIFTRFSKEIQPLIGRILEAVVVRLIKTQNISTEQ
NLLSVLCFLTCNDPKQTVDFLSSFQIDNTDALTLVMRKWIEAFEVIRGEKRIKENIVALS
NLFFLNDKRLQKVVVNGNLIPYEGDLIITRSMAKKMPDRYVQVPLYTKIIKLFVSELSFQ
SKQPNPEQLITSDIKQEVVNANKDDDNDDWEDVDDVLDYDKLKEYIDDDVDEEADDDSDD
ITGLMDVKESVVQLLVRFFKEVASKDVSGFHCIYETLSDSERKVLSEALL
Sequence of entity 2 (B), FASTA
>9B31_2 Histone H2A (chains B)
SGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLA
AEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKK
SAKTAKASQEL
Sequence of entity 3 (C), FASTA
>9B31_3 Histone H2B (chains C)
SSAAEKKPASKAPAEKKPAAKKTSTSVDGKKRSKVRKETYSSYIYKVLKQTHPDTGISQK
SMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRA
VTKYSSSTQA
Sequence of entity 4 (D, E), FASTA
>9B31_4 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 P53067 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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