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- PDB-30fm: Structure of histone H1 in an import-chaperone complex with impor... -

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Basic information

Entry
Database: PDB / ID: 30fm
TitleStructure of histone H1 in an import-chaperone complex with importin beta and importin 7 (full-length model)
Components
  • Histone H1.0
  • Importin 7 L homeolog
  • Importin subunit beta-1
KeywordsTRANSPORT PROTEIN / Importin 7 / histone H1 / Importin beta
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 / positive regulation of transcription regulatory region DNA binding / establishment of mitotic spindle localization / Transport of Ribonucleoproteins into the Host Nucleus / astral microtubule organization / negative regulation of DNA recombination ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / regulation of cholesterol biosynthetic process / endoplasmic reticulum tubular network / positive regulation of transcription regulatory region DNA binding / establishment of mitotic spindle localization / Transport of Ribonucleoproteins into the Host Nucleus / astral microtubule organization / negative regulation of DNA recombination / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / NS1 Mediated Effects on Host Pathways / Initiation of Nuclear Envelope (NE) Reformation / chromosome condensation / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / NLS-bearing protein import into nucleus / ribosomal protein import into nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / minor groove of adenine-thymine-rich DNA binding / Maturation of hRSV A proteins / mitotic spindle assembly / mitotic metaphase chromosome alignment / nuclear pore / transcription repressor complex / nucleosome binding / protein import into nucleus / Assembly of the ORC complex at the origin of replication / Maturation of DENV proteins / chromatin DNA binding / euchromatin / positive regulation of cholesterol biosynthetic process / Hsp90 protein binding / specific granule lumen / small GTPase binding / ISG15 antiviral mechanism / nucleosomal DNA binding / cytoplasmic stress granule / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / structural constituent of chromatin / nucleosome / nuclear envelope / nucleosome assembly / nuclear membrane / double-stranded DNA binding / heterochromatin formation / ficolin-1-rich granule lumen / nuclear body / chromosome / protein domain specific binding / nucleolus / Neutrophil degranulation / chromatin / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / extracellular region / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Exportin-2, central domain / Cse1 / : / Importin-11-like, TPR repeats / : / Importin subunit beta-1-like, TPR repeats / Importin beta family / Linker histone H1/H5 / HEAT-like repeat / linker histone H1 and H5 family ...Exportin-2, central domain / Cse1 / : / Importin-11-like, TPR repeats / : / Importin subunit beta-1-like, TPR repeats / Importin beta family / Linker histone H1/H5 / HEAT-like repeat / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Importin 7 L homeolog / Histone H1.0 / Importin subunit beta-1
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 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed ..._citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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: Importin subunit beta-1
C: Histone H1.0


Theoretical massNumber of molelcules
Total (without water)237,7953
Polymers237,7953
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Single-particle cryo-EM reconstruction of the Importin 7-Importin beta-Histone H1.0 import 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
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 Importin subunit beta-1 / Importin-90 / Karyopherin subunit beta-1 / Nuclear factor p97 / Pore targeting complex 97 kDa subunit / PTAC97


Mass: 97257.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Importin beta / Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB1, NTF97 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14974
#3: Protein Histone H1.0 / Histone H1' / Histone H1(0)


Mass: 20984.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Histone H1.0 / Source: (gene. exp.) Homo sapiens (human) / Gene: H1-0, H1F0, H1FV / Production host: Escherichia coli (E. coli) / References: UniProt: P07305
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: Ternary complex of histone H1.0 with Importin 7 and Importin beta
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.237 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 1.4 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 1.4 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: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12036
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
10RELION5.0.1initial Euler assignment
11RELION5.0.1final Euler assignment
12RELION5.0.1classification
13RELION5.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 901494
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 390745 / Symmetry type: POINT

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