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- EMDB-49114: Cryo-EM structure of human importin beta:Ran-GTP:RanBP1 trimeric ... -

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Basic information

Entry
Database: EMDB / ID: EMD-49114
TitleCryo-EM structure of human importin beta:Ran-GTP:RanBP1 trimeric complex
Map data
Sample
  • Complex: Importin Beta/RanGTP/RanBP1 complex
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: Ran-specific GTPase-activating protein
    • Protein or peptide: GTP-binding nuclear protein Ran
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsImportins / TRANSPORT PROTEIN / Ran / RanBP1
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / regulation of cholesterol biosynthetic process / 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 ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / regulation of cholesterol biosynthetic process / 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 / Transport of Ribonucleoproteins into the Host Nucleus / astral microtubule organization / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Apoptosis induced DNA fragmentation / NS1 Mediated Effects on Host Pathways / Initiation of Nuclear Envelope (NE) Reformation / Rev-mediated nuclear export of HIV RNA / nuclear export / Nuclear import of Rev protein / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / ribosomal protein import into nucleus / GTP metabolic process / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / GDP-dissociation inhibitor activity / MicroRNA (miRNA) biogenesis / spermatid development / DNA metabolic process / male germ cell nucleus / dynein intermediate chain binding / mitotic sister chromatid segregation / Maturation of hRSV A proteins / viral process / mitotic spindle assembly / nuclear pore / ribosomal large subunit export from nucleus / mitotic metaphase chromosome alignment / protein export from nucleus / ribosomal subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / centriole / protein import into nucleus / hippocampus development / Assembly of the ORC complex at the origin of replication / mitotic spindle organization / GTPase activator activity / Maturation of DENV proteins / positive regulation of protein import into nucleus / Transcriptional regulation by small RNAs / positive regulation of cholesterol biosynthetic process / Hsp90 protein binding / recycling endosome / specific granule lumen / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / melanosome / GDP binding / nuclear envelope / mitotic cell cycle / nuclear membrane / midbody / G protein activity / 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 / chromatin binding / GTPase activity / Neutrophil degranulation / nucleolus / GTP binding / protein-containing complex binding / chromatin / magnesium ion binding / enzyme binding / signal transduction / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / membrane / nucleus / cytosol / 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, type 2 / HEAT repeat profile. / 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
Ran-specific GTPase-activating protein / GTP-binding nuclear protein Ran / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsKo Y / Cingolani G
Funding support United States, 1 items
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
DepositionFeb 7, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49114.png

Downloads & links

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Map

FileDownload / File: emd_49114.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesX (Sec.)Y (Row.)Z (Col.)
0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.5
Minimum - Maximum-30.406867999999999 - 56.644226000000003
Average (Standard dev.)-0.000042647673 (±0.9490656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49114_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49114_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Importin Beta/RanGTP/RanBP1 complex

EntireName: Importin Beta/RanGTP/RanBP1 complex
Components
  • Complex: Importin Beta/RanGTP/RanBP1 complex
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: Ran-specific GTPase-activating protein
    • Protein or peptide: GTP-binding nuclear protein Ran
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Importin Beta/RanGTP/RanBP1 complex

SupramoleculeName: Importin Beta/RanGTP/RanBP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Importin subunit beta-1

MacromoleculeName: Importin subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.323922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARR EVKNYVLHTL GTETYRPSSA SQCVAGIACA EIPVNQWPEL IPQLVANVTN PNSTEHMKES TLEAIGYICQ D IDPEQLQD ...String:
MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARR EVKNYVLHTL GTETYRPSSA SQCVAGIACA EIPVNQWPEL IPQLVANVTN PNSTEHMKES TLEAIGYICQ D IDPEQLQD KSNEILTAII QGMRKEEPSN NVKLAATNAL LNSLEFTKAN FDKESERHFI MQVVCEATQC PDTRVRVAAL QN LVKIMSL YYQYMETYMG PALFAITIEA MKSDIDEVAL QGIEFWSNVC DEEMDLAIEA SEAAEQGRPP EHTSKFYAKG ALQ YLVPIL TQTLTKQDEN DDDDDWNPCK AAGVCLMLLA TCCEDDIVPH VLPFIKEHIK NPDWRYRDAA VMAFGCILEG PEPS QLKPL VIQAMPTLIE LMKDPSVVVR DTAAWTVGRI CELLPEAAIN DVYLAPLLQC LIEGLSAEPR VASNVCWAFS SLAEA AYEA ADVADDQEEP ATYCLSSSFE LIVQKLLETT DRPDGHQNNL RSSAYESLME IVKNSAKDCY PAVQKTTLVI MERLQQ VLQ MESHIQSTSD RIQFNDLQSL LCATLQNVLR KVQHQDALQI SDVVMASLLR MFQSTAGSGG VQEDALMAVS TLVEVLG GE FLKYMEAFKP FLGIGLKNYA EYQVCLAAVG LVGDLCRALQ SNIIPFCDEV MQLLLENLGN ENVHRSVKPQ ILSVFGDI A LAIGGEFKKY LEVVLNTLQQ ASQAQVDKSD YDMVDYLNEL RESCLEAYTG IVQGLKGDQE NVHPDVMLVQ PRVEFILSF IDHIAGDEDH TDGVVACAAG LIGDLCTAFG KDVLKLVEAR PMIHELLTEG RRSKTNKAKT LARWATKELR KLKNQA

UniProtKB: Importin subunit beta-1

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Macromolecule #2: Ran-specific GTPase-activating protein

MacromoleculeName: Ran-specific GTPase-activating protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.960367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HFQAVVPAPD EQEIATLEED EEELFCNRAK LFRFASENDL PEWKERGTGD VKLLKHKEKG AIRLLMRRDK TLKICANHYI TPMMELKPN AGSDRAWVWN THADFADECP KPELLAIRFL NAENAQKFKT KFEECRKEIE EREKK

UniProtKB: Ran-specific GTPase-activating protein

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Macromolecule #3: GTP-binding nuclear protein Ran

MacromoleculeName: GTP-binding nuclear protein Ran / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.81042 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EPQVQFKLVL VGDGGTGKTT FVKRHLTGEF EKKYVATLGV EVHPLVFHTN RGPIKFNVWD TAGQEKFGGL RDGYYIQAQC AIIMFDVTS RVTYKNVPNW HRDLVRVCEN IPIVLCGNKV DIKDRKVKAK SIVFHRKKNL QYYDISAKSN YNFEKPFLWL A RKLIGDPN ...String:
EPQVQFKLVL VGDGGTGKTT FVKRHLTGEF EKKYVATLGV EVHPLVFHTN RGPIKFNVWD TAGQEKFGGL RDGYYIQAQC AIIMFDVTS RVTYKNVPNW HRDLVRVCEN IPIVLCGNKV DIKDRKVKAK SIVFHRKKNL QYYDISAKSN YNFEKPFLWL A RKLIGDPN LEFVAMPALA PPEVVMDPAL AAQYEHDLEV AQTTALPEED AA

UniProtKB: GTP-binding nuclear protein Ran

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1qgk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 721883
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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