9YB5: Human importin Beta:Ran-GDP:RanBP1 complex

Cryo-EM structure of human importin Beta:Ran-GDP:RanBP1 complex. Determined by electron microscopy at 3.2 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,402
Mol. weight: 91.36 kDa
Ligands: GDP, MG
Released: 10 Dec 2025

Explore 9YB5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YB5 contains 40 α-helices and 17 β-strands across 3 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 B: 29 helices, 0 β-strands

Element	Residues	Length
α-helix	3-9	7
α-helix	15-31	17
α-helix	33-45	13
α-helix	51-63	13
α-helix	70-81	12
α-helix	85-97	13
α-helix	108-120	13
α-helix	121-123	3
α-helix	129-138	10
α-helix	144-160	17
α-helix	163-166	4
α-helix	170-181	12
α-helix	188-200	13
α-helix	203-205	3
α-helix	206-210	5
α-helix	212-225	14
α-helix	231-247	17
α-helix	249-251	3
α-helix	260-269	10
α-helix	273-300	28
α-helix	314-317	4
α-helix	319-331	13
α-helix	344-359	16
α-helix	360-362	3
α-helix	363-374	12
α-helix	380-392	13
α-helix	409-416	8
α-helix	422-442	21
α-helix	449-458	10

Chain C: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	37-50	14	4
β-strand	59-72	14	4
β-strand	78-83	6	4
β-strand	90-95	6	4
β-strand	112-119	8	4
β-strand	126-133	8	4
α-helix	138-159	22

Chain D: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	1
β-strand	18	1	2
β-strand	20	1	2
α-helix	26-31	6
β-strand	47-54	8	1
β-strand	57-65	9	1
β-strand	85-91	7	1
α-helix	95-99	5
α-helix	101-111	11
β-strand	117-122	6	1
α-helix	133-135	3
α-helix	138-141	4
β-strand	145-148	4	1
β-strand	150	1	3
β-strand	155	1	3
α-helix	159-169	11
β-strand	176	1	1
α-helix	178-180	3
α-helix	183-186	4
α-helix	191-206	16
α-helix	208-214	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Importin subunit beta-1	B	protein	458	Homo sapiens	Q14974 (AlphaFold model)
GTP-binding nuclear protein Ran	D	protein	210	Homo sapiens	P62826 (AlphaFold model)
Ran-specific GTPase-activating protein	C	protein	136	Homo sapiens	P43487 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9YB5_1 Importin subunit beta-1 (chains B)
ELITILEKTVSPDRLELEAAQKFLERAAVENLPTFLVELSRVLANPGNSQVARVAAGLQI
KNSLTSKDPDIKAQYQQRWLAIDANARREVKNYVLQTLGTETYRPSSASQCVAGIACAEI
PVNQWPELIPQLVANVTNPNSTEHMKESTLEAIGYICQDIDPEQLQDKSNEILTAIIQGM
RKEEPSNNVKLAATNALLNSLEFTKANFDKESERHFIMQVVCEATQCPDTRVRVAALQNL
VKIMSLYYQYMETYMGPALFAITIEAMKSDIDEVALQGIEFWSNVCDEEMDLAIEASEAA
EQGRPPEHTSKFYAKGALQYLVPILTQTLTKQDENDDDDDWNPCKAAGVCLMLLATCCED
DIVPHVLPFIKEHIKNPDWRYRDAAVMAFGCILEGPEPSQLKPLVIQAMPTLIELMKDPS
VVVRDTAAWTVGRICELLPEAAINDVYLAPLLQCLIEG

Sequence of entity 2 (D), FASTA

>9YB5_2 GTP-binding nuclear protein Ran (chains D)
AAQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWD
TAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVD
IKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPP
EVVMDPALAAQYEHDLEVAQTTALPDEDAA

Sequence of entity 3 (C), FASTA

>9YB5_3 Ran-specific GTPase-activating protein (chains C)
PDEQEIATLEEDEEELFCNRAKLFRFASENDLPEWKERGTGDVKLLKHKEKGAIRLLMRR
DKTLKICANHYITPMMELKPNAGSDRAWVWNTHADFADECPKPELLAIRFLNAENAQKFK
TKFEECRKEIEEREKK

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1

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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