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- EMDB-57539: Structure of histone H1 in an import-chaperone complex with impor... -

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Basic information

Entry
Database: EMDB / ID: EMD-57539
TitleStructure of histone H1 in an import-chaperone complex with importin beta and importin 7
Map data
Sample
  • Complex: Ternary complex of histone H1.0 with Importin 7 and Importin beta
    • Protein or peptide: Importin 7 L homeolog
    • Protein or peptide: Importin beta
    • Protein or peptide: histone H1
KeywordsImportin 7 / histone H1 / Importin beta / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFu Z / Freytag B / Huyton T / Gorlich D
Funding support Germany, 1 items
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 / Freytag B / Huyton T / Gorlich D
History
DepositionApr 20, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57539.png

Downloads & links

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Map

FileDownload / File: emd_57539.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 160 pix.
= 266.88 Å		1.67 Å/pix.
x 160 pix.
= 266.88 Å		1.67 Å/pix.
x 160 pix.
= 266.88 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0014
Minimum - Maximum-0.009152168 - 0.01803457
Average (Standard dev.)0.00004510151 (±0.00044313495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 266.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57539_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_57539_half_map_1.map
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Half map: #2

Fileemd_57539_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ternary complex of histone H1.0 with Importin 7 and Importin beta

EntireName: Ternary complex of histone H1.0 with Importin 7 and Importin beta
Components
  • Complex: Ternary complex of histone H1.0 with Importin 7 and Importin beta
    • Protein or peptide: Importin 7 L homeolog
    • Protein or peptide: Importin beta
    • Protein or peptide: histone H1

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Supramolecule #1: Ternary complex of histone H1.0 with Importin 7 and Importin beta

SupramoleculeName: Ternary complex of histone H1.0 with Importin 7 and Importin beta
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 237 KDa

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Macromolecule #1: Importin 7 L homeolog

MacromoleculeName: Importin 7 L homeolog / type: protein_or_peptide / ID: 1 / Details: Importin 7 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDPNILIEAL RGTMDPALRE AAERQLNESH KSLHFVSTLL QITMSEQLEL PVRQAGVIYL KNMITQYWPD REVTPGELPP HTIPEEDRHC IRENIVEAIM HSPELIRVQL TTCIHHIIKH DYPNRWTAVV EKIGFYLQSD NSACWLGILL CLYQLVKNYE YKKPEERSPL ...String:
MDPNILIEAL RGTMDPALRE AAERQLNESH KSLHFVSTLL QITMSEQLEL PVRQAGVIYL KNMITQYWPD REVTPGELPP HTIPEEDRHC IRENIVEAIM HSPELIRVQL TTCIHHIIKH DYPNRWTAVV EKIGFYLQSD NSACWLGILL CLYQLVKNYE YKKPEERSPL IAAMQHFLPM LKDRYIQLLA DPSEQSVLIQ KQIFKIFYAL VQYTLPLELI NQQNLAEWIE ILKTVVDRDV PAETLQVDED DRPELPWWKC KKWALHILAR LFERYGSPGN VSKEYNDFAE VFLKAFAVGV QQVLLKVLYQ YKEKQYIAPR VLQQTLNYFN QGVSHAVTWK NLKPHIQGII QDVIFPLMCY TDSDEDLWQE DPYEYIRMKF DVFEDFISPT TAAQTLLFTS CSKRKEVLQK TMGFCYQILT EPAADPRKKD GALHMIGSLA EILLKKKIYK DQMEFMLQNH VFPLFSSELG YMRARACWVL HYFCEVKFKV DQNLQTALEL TRRCLIDDRE MPVKVEAAIA LQVLISNQEK AKEYIVPFIR PVMQALLHII RETENDDLTN VIQKMICEYS EEVTPIAVEM TQHLAMTFNQ VIQTGPDEEG SDDKAVTAMG ILNTIDTLLS VVEDHKEITQ QLEGICLQVI GTVLQQHVLE FYEEIFSLAH SLTCQQVSPQ MWQLLPLVFD IFQQDGFDYF TDMMPLLHNY VTVDTDTLLS DTKYLEMIYS MCKKILTGVA GEDAECHAAK LLEVVILQCK GRGIDQVIPL FVEAALERLT REVKTSELRT MCLQVAIAAL YYSPPLLFNT LENLRFPNNE EPVTNHFIKQ WLNDVDCFLG LHDRKICVLG LCALIELEQR PQVLNQMSSQ ILPAFLLLFN GLKRAYACHA EQENDSDDDG DGEDDEDAAE LGSDEDDIDE EGQEYLEILA KQAGEDGDDE DWEDDDAEET ALEGYTTLLD DEDTPIDEYQ IFKAIFQKLQ GRDPVWYQAL TQGLNEDQGK QLQDIATLAD QRRAAHESKM IEKHGGYKFN APVVPSTFNF GNPAPGMN

UniProtKB: Importin 7 L homeolog

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Macromolecule #2: Importin beta

MacromoleculeName: Importin beta / type: protein_or_peptide / ID: 2 / Details: Importin beta / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARRE VKNYVLQTLG TETYRPSSAS QCVAGIACAE IPVNQWPELI PQLVANVTNP NSTEHMKEST LEAIGYICQD IDPEQLQDKS ...String:
MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARRE VKNYVLQTLG TETYRPSSAS QCVAGIACAE IPVNQWPELI PQLVANVTNP NSTEHMKEST LEAIGYICQD IDPEQLQDKS NEILTAIIQG MRKEEPSNNV KLAATNALLN SLEFTKANFD KESERHFIMQ VVCEATQCPD TRVRVAALQN LVKIMSLYYQ YMETYMGPAL FAITIEAMKS DIDEVALQGI EFWSNVCDEE MDLAIEASEA AEQGRPPEHT SKFYAKGALQ YLVPILTQTL TKQDENDDDD DWNPCKAAGV CLMLLATCCE DDIVPHVLPF IKEHIKNPDW RYRDAAVMAF GCILEGPEPS QLKPLVIQAM PTLIELMKDP SVVVRDTAAW TVGRICELLP EAAINDVYLA PLLQCLIEGL SAEPRVASNV CWAFSSLAEA AYEAADVADD QEEPATYCLS SSFELIVQKL LETTDRPDGH QNNLRSSAYE SLMEIVKNSA KDCYPAVQKT TLVIMERLQQ VLQMESHIQS TSDRIQFNDL QSLLCATLQN VLRKVQHQDA LQISDVVMAS LLRMFQSTAG SGGVQEDALM AVSTLVEVLG GEFLKYMEAF KPFLGIGLKN YAEYQVCLAA VGLVGDLCRA LQSNIIPFCD EVMQLLLENL GNENVHRSVK PQILSVFGDI ALAIGGEFKK YLEVVLNTLQ QASQAQVDKS DYDMVDYLNE LRESCLEAYT GIVQGLKGDQ ENVHPDVMLV QPRVEFILSF IDHIAGDEDH TDGVVACAAG LIGDLCTAFG KDVLKLVEAR PMIHELLTEG RRSKTNKAKT LATWATKELR KLKNQA

UniProtKB: Importin subunit beta-1

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Macromolecule #3: histone H1

MacromoleculeName: histone H1 / type: protein_or_peptide / ID: 3 / Details: Histone H1.0 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTENSTSAPA AKPKRAKASK KSTDHPKYSD MIVAAIQAEK NRAGSSRQSI QKYIKSHYKV GENADSQIKL SIKRLVTTGV LKQTKGVGAS GSFRLAKSDE PKKSVAFKKT KKEIKKVATP KKASKPKKAA SKAPTKKPKA TPVKKAKKKL AATPKKAKKP KTVKAKPVKA ...String:
MTENSTSAPA AKPKRAKASK KSTDHPKYSD MIVAAIQAEK NRAGSSRQSI QKYIKSHYKV GENADSQIKL SIKRLVTTGV LKQTKGVGAS GSFRLAKSDE PKKSVAFKKT KKEIKKVATP KKASKPKKAA SKAPTKKPKA TPVKKAKKKL AATPKKAKKP KTVKAKPVKA SKPKKAKPVK PKAKSSAKRA GKKK

UniProtKB: Histone H1.0

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.4 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Sample volume: 2 microliters blotting time: 5 s blot force setting: 6.
DetailsThe 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.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12036 / Average electron dose: 50.0 e/Å2
Details: Counting mode, 5 images per hole ( beam-image shift)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 901494
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: the ab-initio 3D model was generated from particles from good 2D classes using RELION (version 5.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.1) / Number images used: 390745
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 5.0.1)
FSC plot (resolution estimation)

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