8F1E: Kap114

Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B. Determined by electron microscopy at 3.28 Å resolution. Released 26 Jul 2023.

Method: Electron microscopy
Resolution: 3.28 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 4
Atoms: 10,174
Mol. weight: 163 kDa
Ligands: GTP, MG
Released: 26 Jul 2023

Explore 8F1E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F1E contains 67 α-helices and 16 β-strands across 4 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: 54 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	15-30	16
α-helix	33-45	13
α-helix	51-68	18
α-helix	84-97	14
α-helix	105-119	15
α-helix	128-141	14
α-helix	144-156	13
α-helix	160	1
α-helix	161-165	5
α-helix	168-181	14
α-helix	187-205	19
α-helix	213-235	23
α-helix	243-262	20
α-helix	271-295	25
α-helix	301-320	20
α-helix	328-341	14
α-helix	344-345	2
α-helix	346-354	9
α-helix	356-364	9
α-helix	372-381	10
α-helix	385-401	17
α-helix	406-420	15
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	523-540	18
α-helix	541-543	3
α-helix	546-561	16
α-helix	571-587	17
α-helix	592-605	14
α-helix	606-608	3
α-helix	614-633	20
α-helix	641-655	15
α-helix	663-664	2
α-helix	665-679	15
α-helix	685-700	16
α-helix	704-707	4
α-helix	708-710	3
α-helix	711-722	12
α-helix	728-730	3
α-helix	734-744	11
α-helix	750-766	17
α-helix	770-786	17
α-helix	788-797	10
β-strand	799	1	1
β-strand	804	1	1
α-helix	805-817	13
α-helix	823-839	17
α-helix	842-846	5
β-strand	849	1	2
β-strand	853	1	3
β-strand	874	1	3
β-strand	877	1	2
α-helix	879-893	15
α-helix	965-979	15
α-helix	984-990	7
α-helix	993-1002	10

Chain B: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	29-38	10
β-strand	43-44	2	4
α-helix	47-73	27
α-helix	81-90	10
α-helix	92-98	7

Chain C: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	42-51	10
α-helix	59-87	29
β-strand	91-92	2	4
α-helix	94-104	11
α-helix	108-125	18

Chain D: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	5
α-helix	26-33	8
β-strand	47-54	8	5
β-strand	56	1	6
β-strand	61-68	8	5
α-helix	78-81	4
β-strand	87-93	7	5
α-helix	97-113	17
β-strand	119-124	6	5
α-helix	139-142	4
β-strand	147-150	4	5
α-helix	161-171	11
β-strand	178	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Importin subunit beta-5	A	protein	1004	Saccharomyces cerevisiae S288C	P53067 (AlphaFold model)
Histone H2A.2	B	protein	131	Saccharomyces cerevisiae S288C	P04912 (AlphaFold model)
Histone H2B.2	C	protein	130	Saccharomyces cerevisiae S288C	P02294 (AlphaFold model)
GTP-binding nuclear protein GSP1/CNR1	D	protein	179	Saccharomyces cerevisiae S288C	P32835 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8F1E_1 Importin subunit beta-5 (chains A)
MDINELIIGAQSADKHTREVAETQLLQWCDSDASQVFKALANVALQHEASLESRQFALLS
LRKLITMYWSPGFESYRSTSNVEIDVKDFIREVLLKLCLNDNENTKIKNGASYCIVQISA
VDFPDQWPQLLTVIYDAISHQHSLNAMSLLNEIYDDVVSEEMFFEGGIGLATMEIVFKVL
NTETSTLIAKIAALKLLKACLLQMSSHNEYDEASRKSFVSQCLATSLQILGQLLTLNFGN
VDVISQLKFKSIIYENLVFIKNDFSRKHFSSELQKQFKIMAIQDLENVTHINANVETTES
EPLLETVHDCSIYIVEFLTSVCTLQFSVEEMNKIITSLTILCQLSSETREIWTSDFNTFV
SKETGLAASYNVRDQANEFFTSLPNPQLSLIFKVVSNDIEHSTCNYSTLESLLYLLQCIL
LNDDEITGENIDQSLQILIKTLENILVSQEIPELILARAILTIPRVLDKFIDALPDIKPL
TSAFLAKSLNLALKSDKELIKSATLIAFTYYCYFAELDSVLGPEVCSETQEKVIRIINQV
SSDAEEDTNGALMEVLSQVISYNPKEPHSRKEILQAEFHLVFTISSEDPANVQVVVQSQE
CLEKLLDNINMDNYKNYIELCLPSFINVLDSNNANNYRYSPLLSLVLEFITVFLKKKPND
GFLPDEINQYLFEPLAKVLAFSTEDETLQLATEAFSYLIFNTDTRAMEPRLMDIMKVLER
LLSLEVSDSAAMNVGPLVVAIFTRFSKEIQPLIGRILEAVVVRLIKTQNISTEQNLLSVL
CFLTCNDPKQTVDFLSSFQIDNTDALTLVMRKWIEAFEVIRGEKRIKENIVALSNLFFLN
DKRLQKVVVNGNLIPYEGDLIITRSMAKKMPDRYVQVPLYTKIIKLFVSELSFQSKQPNP
EQLITSDIKQEVVNANKDDDNDDWEDVDDVLDYDKLKEYIDDDVDEEADDDSDDITGLMD
VKESVVQLLVRFFKEVASKDVSGFHCIYETLSDSERKVLSEALL

Sequence of entity 2 (B), FASTA

>8F1E_2 Histone H2A.2 (chains B)
SGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLA
AEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKK
SAKTAKASQEL

Sequence of entity 3 (C), FASTA

>8F1E_3 Histone H2B.2 (chains C)
SSAAEKKPASKAPAEKKPAAKKTSTSVDGKKRSKVRKETYSSYIYKVLKQTHPDTGISQK
SMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRA
VTKYSSSTQA

Sequence of entity 4 (D), FASTA

>8F1E_4 GTP-binding nuclear protein GSP1/CNR1 (chains D)
MSAPAANGEVPTFKLVLVGDGGTGKTTFVKRHLTGEFEKKYIATIGVEVHPLSFYTNFGE
IKFDVWDTAGLEKFGGLRDGYYINAQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIV
LCGNKVDVKERKVKAKTITFHRKKNLQYYDISAKSNYNFEKPFLWLARKLAGNPQLEFV

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

Primary citation

Mechanism of RanGTP priming H2A-H2B release from Kap114 in an atypical RanGTP•Kap114•H2A-H2B complex. Jiou, J., Shaffer, J.M., Bernades, N.E. et al. Proc Natl Acad Sci U S A (2023) 120:e2301199120-e2301199120. DOI 10.1073/pnas.2301199120 · 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
9B3I 2.88 Å, Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114-RanGTP
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
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…

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