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- PDB-6n88: Cryo-EM structure of the Importin7:Importin beta:Histone H1.0 complex -

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Basic information

Entry
Database: PDB / ID: 6n88
TitleCryo-EM structure of the Importin7:Importin beta:Histone H1.0 complex
Components
  • Histone H1.0
  • Importin subunit beta-1
  • MGC52556 protein
KeywordsTRANSPORT PROTEIN / Imp7:ImpB:H1.0 / Importin / Histone H1 / nuclear import / disordered interactions
Function / homologyArmadillo/beta-catenin-like repeat / HEAT repeat profile. / Armadillo / Importin-beta, N-terminal domain / Linker histone H1/H5, domain H15 / Histone H5 / Armadillo-like helical / Exportin-2, central domain / Armadillo-type fold / HEAT, type 2 ...Armadillo/beta-catenin-like repeat / HEAT repeat profile. / Armadillo / Importin-beta, N-terminal domain / Linker histone H1/H5, domain H15 / Histone H5 / Armadillo-like helical / Exportin-2, central domain / Armadillo-type fold / HEAT, type 2 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Importin beta family / Importin-beta N-terminal domain / Cse1 / linker histone H1 and H5 family / ISG15 antiviral mechanism / Transport of Ribonucleoproteins into the Host Nucleus / Importin-beta N-terminal domain profile. / Linker histone H1/H5 globular (H15) domain profile. / Nuclear import of Rev protein / NS1 Mediated Effects on Host Pathways / Neutrophil degranulation / rt:r-hsa-211227: / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Ran protein signal transduction / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / modulation by virus of host process / ribosomal protein import into nucleus / negative regulation of DNA recombination / astral microtubule organization / establishment of mitotic spindle localization / nucleosome positioning / negative regulation of chromatin silencing / AT DNA binding / chromosome condensation / mitotic metaphase plate congression / apoptotic DNA fragmentation / chromatin silencing / Ran GTPase binding / positive regulation of transcription regulatory region DNA binding / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nuclear euchromatin / transcriptional repressor complex / regulation of cholesterol biosynthetic process / mitotic spindle assembly / nuclear pore / nuclear periphery / nucleosomal DNA binding / protein transporter activity / host cell / intracellular transport of virus / Hsp90 protein binding / nucleosome / protein import into nucleus / nucleosome assembly / chromatin DNA binding / cytoplasmic stress granule / actin cytoskeleton / establishment of protein localization / nuclear envelope / specific granule lumen / double-stranded DNA binding / nuclear body / nuclear membrane / ficolin-1-rich granule lumen / nuclear chromatin / protein domain specific binding / regulation of transcription, DNA-templated / neutrophil degranulation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / RNA binding / zinc ion binding / extracellular exosome / membrane / nucleoplasm / extracellular region / nucleus / cytosol / cytoplasm / MGC52556 protein / Histone H1.0 / Importin subunit beta-1
Function and homology information
Specimen sourceXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.2 Å resolution
AuthorsBilokapic, S. / Ivic, N. / Halic, M.
Funding supportGermany , Croatia, 2 items
OrganizationGrant numberCountry
European Research CouncilERC-smallRNAhet-309584Germany
European Communitys Seventh Framework ProgrammeNEWFELPRO_26Croatia
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 28, 2018 / Release: Feb 27, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 27, 2019Structure modelrepositoryInitial release
1.1Mar 13, 2019Structure modelData collection / Database referencescitation / citation_author / em_admin / pdbx_database_proc_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

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Structure visualization

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Assembly

Deposited unit
A: MGC52556 protein
B: Importin subunit beta-1
C: Histone H1.0


Theoretical massNumber of molelcules
Total (without water)237,7383
Polyers237,7383
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide MGC52556 protein / RanBP7


Mass: 119553.156 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: ipo7, MGC52556 / Production host: Escherichia coli (E. coli) / References: UniProt: O42480
#2: Protein/peptide 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: (gene. exp.) Homo sapiens (human) / Gene: KPNB1, NTF97 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14974
#3: Protein/peptide Histone H1.0 / Histone H1' / Histone H1(0)


Mass: 20927.182 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: H1F0, H1FV / Production host: Escherichia coli (E. coli) / References: UniProt: P07305

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Imp7:ImpB:H1.0 / Type: COMPLEX / Entity ID: 1, 2, 3 / 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18900 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066500
ELECTRON MICROSCOPYf_angle_d1.9168238
ELECTRON MICROSCOPYf_dihedral_angle_d4.2051866
ELECTRON MICROSCOPYf_chiral_restr0.07364
ELECTRON MICROSCOPYf_plane_restr0.0121620

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