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- PDB-6n89: Cryo-EM structure of the Importin beta:Histone H1.0 complex -

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Basic information

Entry
Database: PDB / ID: 6n89
TitleCryo-EM structure of the Importin beta:Histone H1.0 complex
Components
  • Histone H1.0
  • Importin subunit beta-1
KeywordsTRANSPORT PROTEIN / Imp7:ImpB:H1.0 / Importin / Histone H1 / nuclear import / disordered interactions
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 / positive regulation of transcription regulatory region DNA binding / astral microtubule organization / establishment of mitotic spindle localization / Transport of Ribonucleoproteins into the Host Nucleus / negative regulation of DNA recombination / Regulation of cholesterol biosynthesis by SREBP (SREBF) ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / positive regulation of transcription regulatory region DNA binding / astral microtubule organization / establishment of mitotic spindle localization / Transport of Ribonucleoproteins into the Host Nucleus / negative regulation of DNA recombination / 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 / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / Nuclear import of Rev protein / chromosome condensation / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitotic metaphase chromosome alignment / minor groove of adenine-thymine-rich DNA binding / mitotic spindle assembly / nuclear pore / nucleosome binding / transcription repressor complex / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / positive regulation of cholesterol biosynthetic process / euchromatin / chromatin DNA binding / ISG15 antiviral mechanism / small GTPase binding / specific granule lumen / protein import into nucleus / cytoplasmic stress granule / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / structural constituent of chromatin / nuclear envelope / nucleosome / heterochromatin formation / nucleosome assembly / actin cytoskeleton / double-stranded DNA binding / nuclear membrane / ficolin-1-rich granule lumen / nuclear body / protein domain specific binding / Neutrophil degranulation / chromatin / enzyme binding / Golgi apparatus / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Importin beta family / HEAT-like repeat / Linker histone H1/H5 / 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 family / HEAT-like repeat / Linker histone H1/H5 / 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 repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeat / 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
Histone H1.0 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsBilokapic, S. / Ivic, N. / Halic, M.
Funding supportEuropean Union, Croatia, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-smallRNAhet-309584European Union
European Communitys Seventh Framework ProgrammeNEWFELPRO_26 Croatia
CitationJournal: Mol Cell / Year: 2019
Title: Fuzzy Interactions Form and Shape the Histone Transport Complex.
Authors: Nives Ivic / Mia Potocnjak / Victor Solis-Mezarino / Franz Herzog / Silvija Bilokapic / Mario Halic /
Abstract: Protein transport into the nucleus is mediated by transport receptors. Import of highly charged proteins, such as histone H1 and ribosomal proteins, requires a dimer of two transport receptors. In ...Protein transport into the nucleus is mediated by transport receptors. Import of highly charged proteins, such as histone H1 and ribosomal proteins, requires a dimer of two transport receptors. In this study, we determined the cryo-EM structure of the Imp7:Impβ:H1.0 complex, showing that the two importins form a cradle that accommodates the linker histone. The H1.0 globular domain is bound to Impβ, whereas the acidic loops of Impβ and Imp7 chaperone the positively charged C-terminal tail. Although it remains disordered, the H1 tail serves as a zipper that closes and stabilizes the structure through transient non-specific interactions with importins. Moreover, we found that the GGxxF and FxFG motifs in the Imp7 C-terminal tail are essential for Imp7:Impβ dimerization and H1 import, resembling importin interaction with nucleoporins, which, in turn, promote complex disassembly. The architecture of many other complexes might be similarly defined by rapidly exchanging electrostatic interactions mediated by disordered regions.
History
DepositionNov 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Feb 27, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 27, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Importin subunit beta-1
B: Histone H1.0


Theoretical massNumber of molelcules
Total (without water)118,1852
Polymers118,1852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: 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
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB1, NTF97 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14974
#2: Protein Histone H1.0 / Histone H1' / Histone H1(0)


Mass: 20927.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 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: Imp7:ImpB:H1.0 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15800 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0083786
ELECTRON MICROSCOPYf_angle_d1.7074729
ELECTRON MICROSCOPYf_dihedral_angle_d3.764945
ELECTRON MICROSCOPYf_chiral_restr00
ELECTRON MICROSCOPYf_plane_restr0.01945

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