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- EMDB-0367: Cryo-EM structure of the Importin beta:Histone H1.0 complex -

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Entry
Database: EMDB / ID: 0367
TitleCryo-EM structure of the Importin beta:Histone H1.0 complex
Map dataImpB:H1 complex
SampleImp7:ImpB:H1.0:
Importin subunit beta-1 / Histone H1.0
Function / homologyImportin-beta N-terminal domain / Regulation of cholesterol biosynthesis by SREBP (SREBF) / linker histone H1 and H5 family / Importin beta family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / HEAT, type 2 / Armadillo-type fold / Armadillo-like helical / Histone H5 ...Importin-beta N-terminal domain / Regulation of cholesterol biosynthesis by SREBP (SREBF) / linker histone H1 and H5 family / Importin beta family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / HEAT, type 2 / Armadillo-type fold / Armadillo-like helical / Histone H5 / Linker histone H1/H5, domain H15 / Importin-beta, N-terminal domain / Armadillo / Importin-beta N-terminal domain profile. / HEAT repeat profile. / ISG15 antiviral mechanism / Linker histone H1/H5 globular (H15) domain profile. / NS1 Mediated Effects on Host Pathways / Transport of Ribonucleoproteins into the Host Nucleus / Neutrophil degranulation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / rt:r-hsa-211227: / Nuclear import of Rev protein / 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 / establishment of mitotic spindle localization / astral microtubule organization / nucleosome positioning / negative regulation of chromatin silencing / chromosome condensation / AT DNA binding / 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 / Histone H1.0 / Importin subunit beta-1
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 7.5 Å resolution
AuthorsBilokapic S / Ivic N / Halic M
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 ReportPDB-ID: 6n89

SummaryFull reportAbout validation report
DateDeposition: Nov 28, 2018 / Header (metadata) release: Dec 12, 2018 / Map release: Feb 27, 2019 / Last update: Mar 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6n89
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0367.map.gz (map file in CCP4 format, 18967 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
168 pix
1.43 Å/pix.
= 240.24 Å
168 pix
1.43 Å/pix.
= 240.24 Å
168 pix
1.43 Å/pix.
= 240.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density
Contour Level:0.034 (by author), 0.034 (movie #1):
Minimum - Maximum-0.042742528 - 0.12378182
Average (Standard dev.)-0.000018629058 (0.0062811677)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions168168168
Origin0.00.00.0
Limit167.0167.0167.0
Spacing168168168
CellA=B=C: 240.23999 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z240.240240.240240.240
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0430.124-0.000

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Supplemental data

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Sample components

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Entire Imp7:ImpB:H1.0

EntireName: Imp7:ImpB:H1.0 / Number of components: 3

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Component #1: protein, Imp7:ImpB:H1.0

ProteinName: Imp7:ImpB:H1.0 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Importin subunit beta-1

ProteinName: Importin subunit beta-1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 97.257812 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Histone H1.0

ProteinName: Histone H1.0 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.927182 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 BASE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 15800
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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