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- EMDB-44412: Cryo-EM structure of human importin beta-Ran-GTP heterodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-44412
TitleCryo-EM structure of human importin beta-Ran-GTP heterodimer
Map data
Sample
  • Complex: Importin Beta/RanGTP Heterodimer
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: GTP-binding nuclear protein Ran
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
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 / 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 / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / 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 / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / centriole / Assembly of the ORC complex at the origin of replication / protein export from nucleus / mitotic spindle organization / male germ cell nucleus / hippocampus development / Hsp90 protein binding / Transcriptional regulation by small RNAs / positive regulation of cholesterol biosynthetic process / 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 / GTP binding / chromatin / 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 / cytosol / cytoplasm
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
GTP-binding nuclear protein Ran / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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: To Be Published
Title: Cryo-EM structure of human importin beta-Ran-GTP heterodimer
Authors: Ko Y / Cingolani G
History
DepositionApr 4, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44412.png

Downloads & links

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Map

FileDownload / File: emd_44412.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 192 pix.
= 204.864 Å		1.07 Å/pix.
x 192 pix.
= 204.864 Å		1.07 Å/pix.
x 192 pix.
= 204.864 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.2195634 - 0.82933563
Average (Standard dev.)0.018094586 (±0.038565278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 204.86401 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44412_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_44412_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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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: GTP-binding nuclear protein Ran
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Importin Beta/RanGTP Heterodimer

SupramoleculeName: Importin Beta/RanGTP Heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: GTP-binding nuclear protein Ran

MacromoleculeName: GTP-binding nuclear protein Ran / type: protein_or_peptide / ID: 2 / 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: 19.539684 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VQFKLVLVGD GGTGKTTFVK RHLTGEFEKK YVATLGVEVH PLVFHTNRGP IKFNVWDTAG QEKFGGLRDG YYIQAQCAII MFDVTSRVT YKNVPNWHRD LVRVCENIPI VLCGNKVDIK DRKVKAKSIV FHRKKNLQYY DISAKSNYNF EKPFLWLARK L IGDPNLEF AA

UniProtKB: GTP-binding nuclear protein Ran

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1567000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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