9N87: Human importin beta: xIBB complex

Cryo-EM structure of human importin beta: xIBB complex. Determined by electron microscopy at 3.4 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, Xenopus laevis
Chains: 2
Atoms: 7,195
Mol. weight: 102.85 kDa
Released: 10 Dec 2025

Explore 9N87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N87 contains 62 α-helices and 0 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: 60 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	16-21	6
α-helix	23-24	2
α-helix	25-29	5
α-helix	37-40	4
α-helix	51-65	15
α-helix	70-81	12
α-helix	92-98	7
α-helix	109-120	12
α-helix	129-134	6
α-helix	135-137	3
α-helix	144-160	17
α-helix	165-169	5
α-helix	170-177	8
α-helix	189-201	13
α-helix	206-209	4
α-helix	212-224	13
α-helix	231-241	11
α-helix	245-248	4
α-helix	249-254	6
α-helix	256-261	6
α-helix	262-268	7
α-helix	273-303	31
α-helix	306-307	2
α-helix	314-317	4
α-helix	323-330	8
α-helix	344-359	16
α-helix	360-362	3
α-helix	363-374	12
α-helix	380-392	13
α-helix	399-416	18
α-helix	423-438	16
α-helix	440-443	4
α-helix	449-459	11
α-helix	464-470	7
α-helix	478-483	6
α-helix	500-514	15
α-helix	521-523	3
α-helix	524-537	14
α-helix	544-560	17
α-helix	571-592	22
α-helix	597-615	19
α-helix	622-639	18
α-helix	641-643	3
α-helix	644-658	15
α-helix	664-672	9
α-helix	673-677	5
α-helix	678-681	4
α-helix	689-701	13
α-helix	709-724	16
α-helix	732-743	12
α-helix	752-777	26
α-helix	783-784	2
α-helix	785-793	9
α-helix	794-806	13
α-helix	814-822	9
α-helix	825-828	4
α-helix	833-836	4
α-helix	842-850	9
α-helix	856-873	18

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	21-41	21
α-helix	42-44	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Importin subunit beta-1	A	protein	876	Homo sapiens	Q14974 (AlphaFold model)
XRIP1a	B	protein	45	Xenopus laevis	A0A2I3HSY1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9N87_1 Importin subunit beta-1 (chains A)
MELITILEKTVSPDRLELEAAQKFLERAAVENLPTFLVELSRVLANPGNSQVARVAAGLQ
IKNSLTSKDPDIKAQYQQRWLAIDANARREVKNYVLQTLGTETYRPSSASQCVAGIACAE
IPVNQWPELIPQLVANVTNPNSTEHMKESTLEAIGYICQDIDPEQLQDKSNEILTAIIQG
MRKEEPSNNVKLAATNALLNSLEFTKANFDKESERHFIMQVVCEATQCPDTRVRVAALQN
LVKIMSLYYQYMETYMGPALFAITIEAMKSDIDEVALQGIEFWSNVCDEEMDLAIEASEA
AEQGRPPEHTSKFYAKGALQYLVPILTQTLTKQDENDDDDDWNPCKAAGVCLMLLATCCE
DDIVPHVLPFIKEHIKNPDWRYRDAAVMAFGCILEGPEPSQLKPLVIQAMPTLIELMKDP
SVVVRDTAAWTVGRICELLPEAAINDVYLAPLLQCLIEGLSAEPRVASNVCWAFSSLAEA
AYEAADVADDQEEPATYCLSSSFELIVQKLLETTDRPDGHQNNLRSSAYESLMEIVKNSA
KDCYPAVQKTTLVIMERLQQVLQMESHIQSTSDRIQFNDLQSLLCATLQNVLRKVQHQDA
LQISDVVMASLLRMFQSTAGSGGVQEDALMAVSTLVEVLGGEFLKYMEAFKPFLGIGLKN
YAEYQVCLAAVGLVGDLCRALQSNIIPFCDEVMQLLLENLGNENVHRSVKPQILSVFGDI
ALAIGGEFKKYLEVVLNTLQQASQAQVDKSDYDMVDYLNELRESCLEAYTGIVQGLKGDQ
ENVHPDVMLVQPRVEFILSFIDHIAGDEDHTDGVVACAAGLIGDLCTAFGKDVLKLVEAR
PMIHELLTEGRRSKTNKAKTLATWATKELRKLKNQA

Sequence of entity 2 (B), FASTA

>9N87_2 XRIP1a (chains B)
MAESLRSPRRSLYKLVGSPPWKEAFRQRCLERMRNSRDRLLNRYR

Primary citation

Ran modulates allosteric crosstalk between importin beta surfaces. Ko, Y.H., Li, F., Suinn, S.S. et al. Nat Commun (2025) 16:11425-11425. DOI 10.1038/s41467-025-66255-0 · PubMed

Other PDB entries of the same protein (UniProt Q14974 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1IBR 2.3 Å, Complex of ran with importin beta
1QGR 2.3 Å, Structure of importin beta bound to the ibb domain of importin alpha (II crystal form,…
2P8Q 2.35 Å, Crystal Structure of human Importin beta bound to the Snurportin1 IBB-domain
1QGK 2.5 Å, Structure of importin beta bound to the ibb domain of importin alpha
3W5K 2.6 Å, Crystal structure of Snail1 and importin beta complex
9N85 2.6 Å, Cryo-EM structure of human importin beta:Ran-GTP:RanBP1 trimeric complex
1F59 2.8 Å, Importin-beta-fxfg nucleoporin complex
1O6O 2.8 Å, Importin Beta aa1-442 bound to five FxFG repeats from yeast Nsp1p. Second crystal form
1O6P 2.8 Å, Importin Beta bound to a GLFG Nucleoporin peptide
2QNA 2.84 Å, Crystal structure of human Importin-beta (127-876) in complex with the IBB-domain of…
1M5N 2.9 Å, Crystal structure of HEAT repeats (1-11) of importin b bound to the non-classical…
3LWW 3.15 Å, Structure of an open and closed conformation of Human Importin Beta bound to the…

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