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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 / Nuclear import of Rev protein / chromosome condensation / Postmitotic nuclear pore complex (NPC) reformation / ribosomal protein import into nucleus / nuclear import signal receptor activity / NLS-bearing protein import into nucleus / 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 / transcription repressor complex / mitotic metaphase chromosome alignment / nuclear pore / 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 / ISG15 antiviral mechanism / small GTPase binding / nucleosomal DNA binding / cytoplasmic stress granule / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / structural constituent of chromatin / nuclear envelope / nucleosome / 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 / nucleoplasm / zinc ion binding / 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: Fu, Z. / Chafra, F. / Freytag, B. / Huyton, T. / Gorlich, D.
History
DepositionApr 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

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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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