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- PDB-9yb5: Cryo-EM structure of human importin Beta:Ran-GDP:RanBP1 complex -

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Basic information

Entry
Database: PDB / ID: 9yb5
TitleCryo-EM structure of human importin Beta:Ran-GDP:RanBP1 complex
Components
  • GTP-binding nuclear protein Ran
  • Importin subunit beta-1
  • Ran-specific GTPase-activating protein
KeywordsTRANSPORT PROTEIN / Importins / Ran / Ran binding protein
Function / homology
Function and homology information


positive regulation of mitotic centrosome separation / RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / establishment of mitotic spindle localization / cellular response to mineralocorticoid stimulus ...positive regulation of mitotic centrosome separation / RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / establishment of mitotic spindle localization / cellular response to mineralocorticoid stimulus / manchette / astral microtubule organization / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Rev-mediated nuclear export of HIV RNA / Initiation of Nuclear Envelope (NE) Reformation / Nuclear import of Rev protein / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / ribosomal protein import into nucleus / nuclear import signal receptor activity / protein-containing complex localization / nuclear localization sequence binding / GDP-dissociation inhibitor activity / nucleocytoplasmic transport / NLS-bearing protein import into nucleus / MicroRNA (miRNA) biogenesis / mitotic metaphase chromosome alignment / DNA metabolic process / dynein intermediate chain binding / Maturation of hRSV A proteins / mitotic sister chromatid segregation / viral process / spermatid development / mitotic spindle assembly / ribosomal large subunit export from nucleus / nuclear pore / sperm flagellum / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / protein export from nucleus / Assembly of the ORC complex at the origin of replication / mitotic spindle organization / GTPase activator activity / male germ cell nucleus / hippocampus development / centriole / Transcriptional regulation by small RNAs / Hsp90 protein binding / positive regulation of cholesterol biosynthetic process / positive regulation of protein import into nucleus / recycling endosome / specific granule lumen / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / melanosome / GDP binding / nuclear envelope / mitotic cell cycle / actin cytoskeleton organization / G protein activity / midbody / nuclear membrane / ficolin-1-rich granule lumen / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / Neutrophil degranulation / centrosome / chromatin / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / enzyme binding / signal transduction / protein-containing complex / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
: / Importin subunit beta-1-like, TPR repeats / Ran-specific GTPase-activating protein 1, Ran-binding domain / Importin beta family / HEAT-like repeat / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain ...: / Importin subunit beta-1-like, TPR repeats / Ran-specific GTPase-activating protein 1, Ran-binding domain / Importin beta family / HEAT-like repeat / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Ran GTPase / Small GTPase Ran-type domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeats / Armadillo / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ran-specific GTPase-activating protein / GTP-binding nuclear protein Ran / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKo, Y. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2025
Title: Ran modulates allosteric crosstalk between importin β surfaces.
Authors: Ying-Hui Ko / Fenglin Li / Stephanie S Suinn / Junwei Li / Chun-Feng David Hou / Ravi K Lokareddy / Gino Cingolani /
Abstract: A cellular gradient of the GTPase Ran orchestrates the movement of import and export complexes through the Nuclear Pore Complex (NPC). Ran-GTP modulates two essential activities of importin β during ...A cellular gradient of the GTPase Ran orchestrates the movement of import and export complexes through the Nuclear Pore Complex (NPC). Ran-GTP modulates two essential activities of importin β during nuclear import. On the one hand, it reduces the avidity of importin β for phenylalanine-glycine-rich nucleoporins (FG-nups), thereby facilitating the passage of import complexes through the permeability barrier. On the other hand, it disassembles import complexes, releasing the import cargo into the nucleus. The precise mechanisms by which Ran-GTP modulates importin β activities have remained hypothetical. Leveraging cryogenic electron microscopy (cryo-EM) single-particle analysis, in this paper, we describe five distinct conformational states of importin β in complex with various effectors encountered during an import reaction, specifically IBB-cargos, FG-repeats, Ran-GTP, Ran-GTP:RanBP1, and Ran-GDP:RanBP1. Comparing these states allows us to decipher the conformational landscape of importin β without interference from crystallization agents and lattice forces. By correlating structural data with biochemical activities, we find that Ran-GTP, but not Ran-GDP, constrains the solenoid structure of importin β, closing high-affinity FG-binding pockets and displacing import cargos through allosteric crosstalk between the concave and convex surfaces. We propose that this allosteric mechanism is relevant to other β-karyopherins involved in nuclear import.
History
DepositionSep 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Importin subunit beta-1
D: GTP-binding nuclear protein Ran
C: Ran-specific GTPase-activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3605
Polymers90,8933
Non-polymers4682
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Importin subunit beta-1 / Importin-90 / Karyopherin subunit beta-1 / Nuclear factor p97 / Pore targeting complex 97 kDa subunit / PTAC97


Mass: 51071.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB1, NTF97 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14974
#2: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 23712.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Production host: Escherichia coli (E. coli)
References: UniProt: P62826, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#3: Protein Ran-specific GTPase-activating protein / Ran-binding protein 1 / RanBP1


Mass: 16109.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43487
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: importin Beta:Ran-GDP:RanBP1 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3700 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 241237 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026531
ELECTRON MICROSCOPYf_angle_d0.5058865
ELECTRON MICROSCOPYf_dihedral_angle_d11.2262466
ELECTRON MICROSCOPYf_chiral_restr0.04998
ELECTRON MICROSCOPYf_plane_restr0.0051151

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