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- PDB-9baw: Cryo-EM structure of human importin beta-Ran-GTP heterodimer -

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Basic information

Entry
Database: PDB / ID: 9baw
TitleCryo-EM structure of human importin beta-Ran-GTP heterodimer
Components
  • GTP-binding nuclear protein Ran
  • Importin subunit beta-1
KeywordsTRANSPORT PROTEIN / Importins / Ran
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / astral microtubule organization / pre-miRNA export from nucleus / establishment of mitotic spindle localization / RNA nuclear export complex / snRNA import into nucleus / manchette ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / astral microtubule organization / pre-miRNA export from nucleus / establishment of mitotic spindle localization / RNA nuclear export complex / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus / 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 / NLS-bearing protein import into nucleus / Apoptosis induced DNA fragmentation / nuclear localization sequence binding / Initiation of Nuclear Envelope (NE) Reformation / ribosomal protein import into nucleus / Rev-mediated nuclear export of HIV RNA / protein localization to nucleolus / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / mitotic metaphase chromosome alignment / dynein intermediate chain binding / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / spermatid development / mitotic spindle assembly / viral process / positive regulation of protein binding / sperm flagellum / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / centriole / protein export from nucleus / Assembly of the ORC complex at the origin of replication / mitotic spindle organization / male germ cell nucleus / hippocampus development / Hsp90 protein binding / positive regulation of cholesterol biosynthetic process / Transcriptional regulation by small RNAs / recycling endosome / positive regulation of protein import into nucleus / small GTPase binding / ISG15 antiviral mechanism / specific granule lumen / cytoplasmic stress granule / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / GDP binding / melanosome / nuclear envelope / mitotic cell cycle / G protein activity / actin cytoskeleton organization / midbody / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ficolin-1-rich granule lumen / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / Neutrophil degranulation / chromatin binding / chromatin / GTP binding / protein-containing complex binding / nucleolus / enzyme binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Importin beta family / HEAT-like repeat / 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 ...Importin beta family / HEAT-like repeat / 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 / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein Ran / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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: To Be Published
Title: Cryo-EM structure of human importin beta-Ran-GTP heterodimer
Authors: Ko, Y. / Cingolani, G.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit beta-1
B: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4114
Polymers116,8642
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, 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: 97323.922 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: 19539.684 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 / Variant: Q69L / Production host: Escherichia coli (E. coli)
References: UniProt: P62826, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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/RanGTP Heterodimer / Type: COMPLEX / Entity ID: #1-#2 / 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1567000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038370
ELECTRON MICROSCOPYf_angle_d0.6111362
ELECTRON MICROSCOPYf_dihedral_angle_d12.873125
ELECTRON MICROSCOPYf_chiral_restr0.0421308
ELECTRON MICROSCOPYf_plane_restr0.0051471

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