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- EMDB-49117: Cryo-EM structure of human importin beta: xIBB complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49117
TitleCryo-EM structure of human importin beta: xIBB complex
Map data
Sample
  • Complex: Importin Beta/RanGTP Heterodimer
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: XRIP1a
KeywordsImportins / TRANSPORT PROTEIN / Ran
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 / establishment of mitotic spindle localization / Transport of Ribonucleoproteins into the Host Nucleus / astral microtubule organization / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / regulation of cholesterol biosynthetic process / endoplasmic reticulum tubular network / establishment of mitotic spindle localization / 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 / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / ribosomal protein import into nucleus / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / Maturation of hRSV A proteins / mitotic spindle assembly / nuclear pore / mitotic metaphase chromosome alignment / protein import into nucleus / Assembly of the ORC complex at the origin of replication / Maturation of DENV proteins / positive regulation of cholesterol biosynthetic process / Hsp90 protein binding / specific granule lumen / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / nuclear membrane / ficolin-1-rich granule lumen / protein domain specific binding / Neutrophil degranulation / enzyme binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Importin subunit beta-1-like, TPR repeats / Importin beta family / HEAT-like repeat / 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. ...: / Importin subunit beta-1-like, TPR repeats / Importin beta family / HEAT-like repeat / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKo Y / Li J / 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_49117.png

Downloads & links

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Map

FileDownload / File: emd_49117.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 223.232 Å		0.87 Å/pix.
x 256 pix.
= 223.232 Å		0.87 Å/pix.
x 256 pix.
= 223.232 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.872 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.009907036 - 0.019000746
Average (Standard dev.)0.000037494334 (±0.00051584374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 223.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49117_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_49117_half_map_2.map
Projections & Slices
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Sample components

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Entire : Importin Beta/RanGTP Heterodimer

EntireName: Importin Beta/RanGTP Heterodimer
Components
  • Complex: Importin Beta/RanGTP Heterodimer
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: XRIP1a

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Supramolecule #1: Importin Beta/RanGTP Heterodimer

SupramoleculeName: Importin Beta/RanGTP Heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 97.257812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARR EVKNYVLQTL GTETYRPSSA SQCVAGIACA EIPVNQWPEL IPQLVANVTN PNSTEHMKES TLEAIGYICQ D IDPEQLQD ...String:
MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARR EVKNYVLQTL 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 LATWATKELR KLKNQA

UniProtKB: Importin subunit beta-1

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Macromolecule #2: XRIP1a

MacromoleculeName: XRIP1a / type: protein_or_peptide / ID: 2 / Details: modeled sequence is from Homo sapiens (UNP Q86UA6) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 5.593553 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAESLRSPRR SLYKLVGSPP WKEAFRQRCL ERMRNSRDRL LNRYR

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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: GATAN K3 (6k 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 293677
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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