8H5B: Importin subunit beta-5

The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein. Determined by electron microscopy at 4.03 Å resolution. Released 20 Sept 2023.

Method: Electron microscopy
Resolution: 4.03 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 2
Atoms: 8,570
Mol. weight: 134.14 kDa
Released: 20 Sept 2023

Explore 8H5B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H5B contains 58 α-helices and 14 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 A: 53 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	17-30	14
α-helix	33-45	13
α-helix	51-64	14
α-helix	65-69	5
α-helix	84-99	16
α-helix	105-126	22
α-helix	130-135	6
α-helix	136-141	6
α-helix	144-157	14
α-helix	160-164	5
α-helix	168-181	14
α-helix	187-206	20
α-helix	213-235	23
α-helix	244-263	20
α-helix	266-268	3
α-helix	271-290	20
α-helix	303-320	18
α-helix	328-341	14
α-helix	343-345	3
α-helix	346-354	9
α-helix	356-363	8
α-helix	372-381	10
α-helix	385-402	18
α-helix	406-421	16
α-helix	429-447	19
α-helix	453-469	17
α-helix	477-493	17
α-helix	499-514	16
α-helix	517-520	4
α-helix	523-541	19
α-helix	549-560	12
α-helix	571-587	17
α-helix	592-605	14
α-helix	611-633	23
α-helix	641-655	15
β-strand	663	1	1
α-helix	665-681	17
α-helix	685-701	17
β-strand	702	1	1
α-helix	704-706	3
α-helix	708-721	14
α-helix	728-731	4
α-helix	734-744	11
α-helix	749-766	18
α-helix	770-786	17
α-helix	788-797	10
β-strand	799	1	2
β-strand	804	1	2
α-helix	805-819	15
α-helix	823-837	15
α-helix	842-845	4
α-helix	879-895	17
α-helix	935-940	6
α-helix	965-977	13
α-helix	984-989	6
α-helix	996-999	4

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	64-65	2
β-strand	66-75	10	3
α-helix	82-88	7
β-strand	93	1	3
β-strand	102-105	4	3
β-strand	112-115	4	3
β-strand	120-124	5	3
α-helix	129-145	17
β-strand	156-165	10	3
α-helix	172-179	8
β-strand	184	1	3
β-strand	194-197	4	3
β-strand	202-206	5	3
β-strand	211-215	5	3
α-helix	220-234	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Importin subunit beta-5	A	protein	1004	Saccharomyces cerevisiae S288C	P53067 (AlphaFold model)
TATA-box-binding protein	B	protein	180	Saccharomyces cerevisiae S288C	P13393 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8H5B_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

>8H5B_2 TATA-box-binding protein (chains B)
SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGK
MVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHG
TFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

Primary citation

Structural convergence endows nuclear transport receptor Kap114p with a transcriptional repressor function toward TATA-binding protein. Liao, C.C., Wang, Y.S., Pi, W.C. et al. Nat Commun (2023) 14:5518-5518. DOI 10.1038/s41467-023-41206-9 · 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
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

Browse structure collections

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