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- PDB-30jz: Structure of Importin 7 in complex with RanGTP -

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Basic information

Entry
Database: PDB / ID: 30jz
TitleStructure of Importin 7 in complex with RanGTP
Components
  • GTP-binding nuclear protein Ran
  • Importin 7 L homeolog
KeywordsTRANSPORT PROTEIN / Importin 7 / RanGTP
Function / homology
Function and homology information


RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / protein localization to nucleolus ...RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA / 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 / GTP metabolic process / ribosomal protein import into nucleus / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / spermatid development / DNA metabolic process / male germ cell nucleus / dynein intermediate chain binding / mitotic sister chromatid segregation / viral process / ribosomal large subunit export from nucleus / nuclear pore / protein export from nucleus / ribosomal subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / centriole / protein import into nucleus / hippocampus development / mitotic spindle organization / positive regulation of protein import into nucleus / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / melanosome / GDP binding / mitotic cell cycle / nuclear envelope / cell division / midbody / G protein activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / chromatin binding / GTPase activity / nucleolus / GTP binding / protein-containing complex binding / chromatin / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Exportin-2, central domain / Cse1 / : / Importin-11-like, TPR repeats / 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 ...Exportin-2, central domain / Cse1 / : / Importin-11-like, TPR repeats / 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 / 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 / Importin 7 L homeolog / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFu, Z. / Chafra, F. / Freytag, B. / Huyton, T. / Gorlich, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Structure / Year: 2026
Title: Chaperoning by dynamic encasement: Structural basis of linker histone H1 nuclear import.
Authors: Zhenglin Fu / Fatma Chafra / Bernard Freytag / Trevor Huyton / Dirk Görlich /
Abstract: Importins transport numerous proteins into cell nuclei. They also chaperone highly positively charged cargoes against ionic aggregation during transit. An extreme example is histone H1, which ...Importins transport numerous proteins into cell nuclei. They also chaperone highly positively charged cargoes against ionic aggregation during transit. An extreme example is histone H1, which requires two importins, Importin 7 (Imp7) and Importin β (Impβ), for safe import. Here, we present a combined cryoelectron microscopy (cryo-EM)/molecular dynamics (MD) structure of the Imp7·Impβ·H1 complex, correcting a previous model (PDB 6N88) with misassigned importin chains. Our structure reveals that Imp7 contacts Impβ via three interfaces and that this heterodimerization creates a large negatively charged cavity. The globular H1-domain is recognized by Imp7 alone. The highly cationic C-terminal H1-tail participates in fluid-like transient interactions, contacting the inner surface of Impβ before returning to the α-solenoid and long acidic loop of Imp7. This architecture and dynamics explain how the importins shield the histone's enormous positive charge while avoiding interactions too strong for efficient intranuclear cargo release. Finally, we report a RanGTP·Imp7 structure, illustrating how RanGTP dissociates the import complex inside nuclei.
History
DepositionApr 29, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin 7 L homeolog
B: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,2364
Polymers139,6892
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Single-particle cryo-EM reconstruction of the Importin 7-RanGTP complex. One copy of each protein forms the biological unit, no symmetry beyond C1.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Importin 7 L homeolog / MGC52556 protein / RanBP7


Mass: 119553.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Importin 7 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: ipo7.L, imp7, ipo7, MGC52556, ranbp7 / Production host: Escherichia coli (E. coli) / References: UniProt: O42480
#2: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 20135.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GTP-binding nuclear protein Ran Q69L / Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / 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 / Feature type: SUBJECT OF INVESTIGATION / 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 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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 7 in complex with RanGTP / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The complex was further purified by size exclusion chromatography using a Superdex 200 16/600 column. The purified complex was applied to a glow-discharged grid after being diluted to 0.8 mg/ml.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Sample volume: 2 microliters blotting time: 5 s blot force setting: 6

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 8100 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12532
Details: Counting mode 5 images per hole ( beam-image shift)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
4Warp1.0.9CTF correction
7UCSF Chimeramodel fitting
9RELION5.0.1initial Euler assignment
10RELION5.0.1final Euler assignment
11RELION5.0.1classification
12RELION5.0.13D reconstruction
13PHENIX2.0_5885model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1097208
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 675579 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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