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- EMDB-44492: Cryo-EM structure of importin alpha-1/beta bound to FG repeats -

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Basic information

Entry
Database: EMDB / ID: EMD-44492
TitleCryo-EM structure of importin alpha-1/beta bound to FG repeats
Map data
Sample
  • Complex: Importin Alpha1/Beta Heterodimer
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: Importin subunit alpha-1
    • Protein or peptide: LYS-PRO-ALA-PHE-SER-PHE-GLY
    • Protein or peptide: ALA-PHE-SER-PHE
  • Protein or peptide: PHE-GLY-ALA
  • Ligand: PHENYLALANINE
  • Ligand: GLYCINE
KeywordsImportins / TRANSPORT PROTEIN / FG nucleoporins
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / Sensing of DNA Double Strand Breaks / endoplasmic reticulum tubular network / regulation of DNA recombination / astral microtubule organization / entry of viral genome into host nucleus through nuclear pore complex via importin / establishment of mitotic spindle localization / positive regulation of viral life cycle ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / Sensing of DNA Double Strand Breaks / endoplasmic reticulum tubular network / regulation of DNA recombination / astral microtubule organization / entry of viral genome into host nucleus through nuclear pore complex via importin / establishment of mitotic spindle localization / positive regulation of viral life cycle / 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 / Initiation of Nuclear Envelope (NE) Reformation / Nuclear import of Rev protein / ribosomal protein import into nucleus / Postmitotic nuclear pore complex (NPC) reformation / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / mitotic metaphase chromosome alignment / CaMK IV-mediated phosphorylation of CREB / DNA metabolic process / mitotic spindle assembly / nuclear pore / positive regulation of type I interferon production / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / positive regulation of cholesterol biosynthetic process / small GTPase binding / ISG15 antiviral mechanism / specific granule lumen / histone deacetylase binding / protein import into nucleus / cytoplasmic stress granule / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / host cell / nuclear membrane / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Golgi membrane / protein domain specific binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Importin beta family / HEAT-like repeat / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. ...Importin beta family / HEAT-like repeat / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Importin-alpha, importin-beta-binding domain / IBB domain profile. / HEAT repeat profile. / HEAT, type 2 / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin subunit alpha-1 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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
DepositionApr 17, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44492.png

Downloads & links

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Map

FileDownload / File: emd_44492.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 256 pix.
= 245.504 Å		0.96 Å/pix.
x 256 pix.
= 245.504 Å		0.96 Å/pix.
x 256 pix.
= 245.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.959 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.39511558 - 0.9957259
Average (Standard dev.)-0.0019704506 (±0.031480625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44492_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44492_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Importin Alpha1/Beta Heterodimer

EntireName: Importin Alpha1/Beta Heterodimer
Components
  • Complex: Importin Alpha1/Beta Heterodimer
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: Importin subunit alpha-1
    • Protein or peptide: LYS-PRO-ALA-PHE-SER-PHE-GLY
    • Protein or peptide: ALA-PHE-SER-PHE
  • Protein or peptide: PHE-GLY-ALA
  • Ligand: PHENYLALANINE
  • Ligand: GLYCINE

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Supramolecule #1: Importin Alpha1/Beta Heterodimer

SupramoleculeName: Importin Alpha1/Beta Heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: PHE-GLY-ALA

MacromoleculeName: PHE-GLY-ALA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 293.319 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
FGA

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Macromolecule #2: Importin subunit beta-1

MacromoleculeName: Importin subunit beta-1 / type: protein_or_peptide / ID: 2 / 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 #3: Importin subunit alpha-1

MacromoleculeName: Importin subunit alpha-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.356357 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTNENANTP AARLHRFKNK GKDSTEMRRR RIEVNVELRK AKKDDQMLKR RNV

UniProtKB: Importin subunit alpha-1

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Macromolecule #4: LYS-PRO-ALA-PHE-SER-PHE-GLY

MacromoleculeName: LYS-PRO-ALA-PHE-SER-PHE-GLY / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 753.865 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPAFSFG

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Macromolecule #5: ALA-PHE-SER-PHE

MacromoleculeName: ALA-PHE-SER-PHE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 470.518 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AFSF

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Macromolecule #6: PHENYLALANINE

MacromoleculeName: PHENYLALANINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: PHE
Molecular weightTheoretical: 165.189 Da
Chemical component information

ChemComp-PHE:
PHENYLALANINE

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Macromolecule #7: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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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

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 / 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 593354
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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