9B3I: Yeast (Nap1)2-H2A-H2B-Kap114-RanGTP
Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114-RanGTP. Determined by electron microscopy at 2.88 Å resolution. Released 27 Nov 2024.
- Method
- Electron microscopy
- Resolution
- 2.88 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 6
- Atoms
- 14,951
- Mol. weight
- 260.75 kDa
- Ligands
- GTP, MG
- Released
- 27 Nov 2024
Explore 9B3I in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9B3I contains 109 α-helices and 33 β-strands across 6 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: 59 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-9 | 7 | |
| α-helix | 15-31 | 17 | |
| α-helix | 33-45 | 13 | |
| α-helix | 51-68 | 18 | |
| α-helix | 84-98 | 15 | |
| α-helix | 105-122 | 18 | |
| α-helix | 129-141 | 13 | |
| α-helix | 144-156 | 13 | |
| α-helix | 160-164 | 5 | |
| α-helix | 168-181 | 14 | |
| α-helix | 187-205 | 19 | |
| α-helix | 213-233 | 21 | |
| α-helix | 243-263 | 21 | |
| α-helix | 266-268 | 3 | |
| α-helix | 271-294 | 24 | |
| α-helix | 295-297 | 3 | |
| α-helix | 302-320 | 19 | |
| α-helix | 328-341 | 14 | |
| α-helix | 344-345 | 2 | |
| α-helix | 346-354 | 9 | |
| α-helix | 356-363 | 8 | |
| α-helix | 372-382 | 11 | |
| α-helix | 385-401 | 17 | |
| α-helix | 408-420 | 13 | |
| α-helix | 431-447 | 17 | |
| α-helix | 453-469 | 17 | |
| α-helix | 477-494 | 18 | |
| α-helix | 498-514 | 17 | |
| α-helix | 517-521 | 5 | |
| α-helix | 523-541 | 19 | |
| α-helix | 548-560 | 13 | |
| α-helix | 563-565 | 3 | |
| α-helix | 566-568 | 3 | |
| α-helix | 571-587 | 17 | |
| α-helix | 592-605 | 14 | |
| α-helix | 606-608 | 3 | |
| α-helix | 614-633 | 20 | |
| α-helix | 641-656 | 16 | |
| α-helix | 665-679 | 15 | |
| α-helix | 685-701 | 17 | |
| α-helix | 704-707 | 4 | |
| α-helix | 708-710 | 3 | |
| α-helix | 711-722 | 12 | |
| α-helix | 728-731 | 4 | |
| α-helix | 734-744 | 11 | |
| α-helix | 750-752 | 3 | |
| α-helix | 753-766 | 14 | |
| α-helix | 770-786 | 17 | |
| α-helix | 788-797 | 10 | |
| β-strand | 799-800 | 2 | 1 |
| β-strand | 803-804 | 2 | 1 |
| α-helix | 805-816 | 12 | |
| α-helix | 823-839 | 17 | |
| α-helix | 842-846 | 5 | |
| β-strand | 848 | 1 | 2 |
| β-strand | 852-854 | 3 | 3 |
| α-helix | 855-856 | 2 | |
| α-helix | 864-867 | 4 | |
| β-strand | 873-875 | 3 | 3 |
| β-strand | 878 | 1 | 2 |
| α-helix | 879-893 | 15 | |
| α-helix | 935-940 | 6 | |
| α-helix | 965-979 | 15 | |
| α-helix | 981-990 | 10 | |
| α-helix | 993-1003 | 11 | |
Chain B: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 28-38 | 11 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 47-73 | 27 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-89 | 9 | |
| α-helix | 92-98 | 7 | |
Chain C: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 5 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 4 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-125 | 19 | |
Chain D: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-19 | 8 | 6 |
| α-helix | 25-34 | 10 | |
| β-strand | 47-56 | 10 | 6 |
| β-strand | 59-68 | 10 | 6 |
| α-helix | 79-81 | 3 | |
| β-strand | 87-93 | 7 | 6 |
| α-helix | 97-101 | 5 | |
| α-helix | 103-113 | 11 | |
| β-strand | 119-124 | 6 | 6 |
| α-helix | 140-144 | 5 | |
| β-strand | 147-150 | 4 | 6 |
| α-helix | 161-171 | 11 | |
| β-strand | 178 | 1 | 6 |
Chain E: 18 helices, 8 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 | 7 |
| β-strand | 228-235 | 8 | 7 |
| β-strand | 243 | 1 | 8 |
| β-strand | 247-254 | 8 | 7 |
| α-helix | 258-259 | 2 | |
| α-helix | 260-262 | 3 | |
| α-helix | 264-265 | 2 | |
| β-strand | 266-271 | 6 | 7 |
| β-strand | 276 | 1 | 8 |
| β-strand | 285-293 | 9 | 9 |
| β-strand | 300-308 | 9 | 9 |
| 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 | |
Chain F: 17 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 | 188-194 | 7 | |
| α-helix | 197-200 | 4 | |
| α-helix | 205-211 | 7 | |
| β-strand | 216-221 | 6 | 10 |
| β-strand | 228-234 | 7 | 10 |
| β-strand | 243 | 1 | 11 |
| β-strand | 247-254 | 8 | 10 |
| β-strand | 266-271 | 6 | 10 |
| β-strand | 276 | 1 | 11 |
| β-strand | 285-294 | 10 | 12 |
| β-strand | 299-308 | 10 | 12 |
| α-helix | 312-315 | 4 | |
| α-helix | 323-333 | 11 | |
| α-helix | 334-338 | 5 | |
| α-helix | 339-347 | 9 | |
| α-helix | 348-352 | 5 | |
| α-helix | 353-355 | 3 | |
| α-helix | 356-361 | 6 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| KAP114 isoform 1 | A | protein | 1012 | Saccharomyces cerevisiae | P53067 (AlphaFold model) |
| Histone H2A | B | protein | 131 | Saccharomyces cerevisiae | P04912 (AlphaFold model) |
| Histone H2B | C | protein | 130 | Saccharomyces cerevisiae | P02294 (AlphaFold model) |
| GTP-binding nuclear protein | D | protein | 186 | Saccharomyces cerevisiae | P32835 (AlphaFold model) |
| NAP1 isoform 1 | E, F | protein | 420 | Saccharomyces cerevisiae | P25293 |
Sequence of entity 1 (A), FASTA
>9B3I_1 KAP114 isoform 1 (chains A)
GSPNSRVDMDINELIIGAQSADKHTREVAETQLLQWCDSDASQVFKALANVALQHEASLE
SRQFALLSLRKLITMYWSPGFESYRSTSNVEIDVKDFIREVLLKLCLNDNENTKIKNGAS
YCIVQISAVDFPDQWPQLLTVIYDAISHQHSLNAMSLLNEIYDDVVSEEMFFEGGIGLAT
MEIVFKVLNTETSTLIAKIAALKLLKACLLQMSSHNEYDEASRKSFVSQCLATSLQILGQ
LLTLNFGNVDVISQLKFKSIIYENLVFIKNDFSRKHFSSELQKQFKIMAIQDLENVTHIN
ANVETTESEPLLETVHDCSIYIVEFLTSVCTLQFSVEEMNKIITSLTILCQLSSETREIW
TSDFNTFVSKETGLAASYNVRDQANEFFTSLPNPQLSLIFKVVSNDIEHSTCNYSTLESL
LYLLQCILLNDDEITGENIDQSLQILIKTLENILVSQEIPELILARAILTIPRVLDKFID
ALPDIKPLTSAFLAKSLNLALKSDKELIKSATLIAFTYYCYFAELDSVLGPEVCSETQEK
VIRIINQVSSDAEEDTNGALMEVLSQVISYNPKEPHSRKEILQAEFHLVFTISSEDPANV
QVVVQSQECLEKLLDNINMDNYKNYIELCLPSFINVLDSNNANNYRYSPLLSLVLEFITV
FLKKKPNDGFLPDEINQYLFEPLAKVLAFSTEDETLQLATEAFSYLIFNTDTRAMEPRLM
DIMKVLERLLSLEVSDSAAMNVGPLVVAIFTRFSKEIQPLIGRILEAVVVRLIKTQNIST
EQNLLSVLCFLTCNDPKQTVDFLSSFQIDNTDALTLVMRKWIEAFEVIRGEKRIKENIVA
LSNLFFLNDKRLQKVVVNGNLIPYEGDLIITRSMAKKMPDRYVQVPLYTKIIKLFVSELS
FQSKQPNPEQLITSDIKQEVVNANKDDDNDDWEDVDDVLDYDKLKEYIDDDVDEEADDDS
DDITGLMDVKESVVQLLVRFFKEVASKDVSGFHCIYETLSDSERKVLSEALL
Sequence of entity 2 (B), FASTA
>9B3I_2 Histone H2A (chains B)
SGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLA
AEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKK
SAKTAKASQEL
Sequence of entity 3 (C), FASTA
>9B3I_3 Histone H2B (chains C)
SSAAEKKPASKAPAEKKPAAKKTSTSVDGKKRSKVRKETYSSYIYKVLKQTHPDTGISQK
SMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRA
VTKYSSSTQA
Sequence of entity 4 (D), FASTA
>9B3I_4 GTP-binding nuclear protein (chains D)
MASAPAANGEVPTFKLVLVGDGGTGKTTFVKRHLTGEFEKKYIATIGVEVHPLSFYTNFG
EIKFDVWDTAGLEKFGGLRDGYYINAQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPI
VLCGNKVDVKERKVKAKTITFHRKKNLQYYDISAKSNYNFEKPFLWLARKLAGNPQLEFV
ENLYFQ
Sequence of entity 5 (E, F), FASTA
>9B3I_5 NAP1 isoform 1 (chains E, F)
GSMGTDPIRTKPKSSMQIDNAPTPHNTPASVLNPSYLKNGNPVRAQAQEQDDKIGTINEE
DILANQPLLLQSIQDRLGSLVGQDSGYVGGLPKNVKEKLLSLKTLQSELFEVEKEFQVEM
FELENKFLQKYKPIWEQRSRIISGQEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDS
EEEQVKGIPSFWLTALENLPIVADTITDRDAEVLEYLQDIGLEYLTDGRPGFKLLFRFDS
SANPFFTNDILAKTYFYQKELGYSGDFIYDHAEGAEISWKDNAHNVTVDLEMRKQRNKTT
KQVRTIEKITPIESFFNFFDPPKIQNEDQDEELEEDLEERLALDYSIGEQLKDKLIPRAV
DWFTGAALEFEFEEDEEEADEDEDEEDDDDHGLEDDDGESAEEQDDFAGRPEQAPECKQS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
| MG | Magnesium ion | Mg | 1 |
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:
- 6AHO 2.5 Å, Crystal structure of Kap114p
- 9B31 3.2 Å, Cryo-EM structure of yeast (Nap1)2-Kap114-H2A-H2B
- 8F0X 3.21 Å, Cryo-EM structure of Kap114 bound to H2A-H2B
- 8F1E 3.28 Å, Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B
- 8F19 3.49 Å, Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP)
- 9B3F 3.54 Å, Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114
- 8H5B 4.03 Å, The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box…
Browse structure collections
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