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- EMDB-0366: Imp7:ImpB:H1.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-0366
TitleImp7:ImpB:H1.0
Map dataImp7:Impu03B2:H1
Sample
  • Complex: Imp7:ImpB:H1.0
    • Protein or peptide: MGC52556 protein
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: Histone H1.0
KeywordsImp7:ImpB:H1.0 / Importin / Histone H1 / nuclear import / disordered interactions / TRANSPORT PROTEIN
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 / astral microtubule organization / establishment of mitotic spindle localization / positive regulation of transcription regulatory region DNA binding / negative regulation of DNA recombination / Transport of Ribonucleoproteins into the Host Nucleus / 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 / astral microtubule organization / establishment of mitotic spindle localization / positive regulation of transcription regulatory region DNA binding / negative regulation of DNA recombination / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Nuclear import of Rev protein / chromosome condensation / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / mitotic metaphase chromosome alignment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / NLS-bearing protein import into nucleus / minor groove of adenine-thymine-rich DNA binding / nucleosome binding / mitotic spindle assembly / nuclear pore / nucleosomal DNA binding / transcription repressor complex / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / euchromatin / chromatin DNA binding / heterochromatin formation / ISG15 antiviral mechanism / small GTPase binding / specific granule lumen / cytoplasmic stress granule / protein import into nucleus / structural constituent of chromatin / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nucleosome / actin cytoskeleton / nucleosome assembly / nuclear envelope / double-stranded DNA binding / nuclear membrane / ficolin-1-rich granule lumen / nuclear body / protein domain specific binding / Neutrophil degranulation / chromatin / Golgi apparatus / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Exportin-2, central domain / Cse1 / Importin beta family / 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 / HEAT-like repeat / Importin-beta N-terminal domain profile. ...Exportin-2, central domain / Cse1 / Importin beta family / 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 / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / 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 speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsBilokapic S / Ivic N
Funding supportEuropean Union, Croatia, 2 items
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, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseFeb 27, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0356
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0356
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n88
  • Surface level: 0.0356
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0366.png

Downloads & links

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Map

FileDownload / File: emd_0366.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationImp7:Impu03B2:H1
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0356 / Movie #1: 0.0356
Minimum - Maximum-0.04906157 - 0.14652337
Average (Standard dev.)0.000508653 (±0.007547136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 240.23999 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0490.1470.001

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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
Components
  • Complex: Imp7:ImpB:H1.0
    • Protein or peptide: MGC52556 protein
    • Protein or peptide: Importin subunit beta-1
    • Protein or peptide: Histone H1.0

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Supramolecule #1: Imp7:ImpB:H1.0

SupramoleculeName: Imp7:ImpB:H1.0 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: MGC52556 protein

MacromoleculeName: MGC52556 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 119.553156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDPNILIEAL RGTMDPALRE AAERQLNESH KSLHFVSTLL QITMSEQLEL PVRQAGVIYL KNMITQYWPD REVTPGELPP HTIPEEDRH CIRENIVEAI MHSPELIRVQ LTTCIHHIIK HDYPNRWTAV VEKIGFYLQS DNSACWLGIL LCLYQLVKNY E YKKPEERS ...String:
MDPNILIEAL RGTMDPALRE AAERQLNESH KSLHFVSTLL QITMSEQLEL PVRQAGVIYL KNMITQYWPD REVTPGELPP HTIPEEDRH CIRENIVEAI MHSPELIRVQ LTTCIHHIIK HDYPNRWTAV VEKIGFYLQS DNSACWLGIL LCLYQLVKNY E YKKPEERS PLIAAMQHFL PMLKDRYIQL LADPSEQSVL IQKQIFKIFY ALVQYTLPLE LINQQNLAEW IEILKTVVDR DV PAETLQV DEDDRPELPW WKCKKWALHI LARLFERYGS PGNVSKEYND FAEVFLKAFA VGVQQVLLKV LYQYKEKQYI APR VLQQTL NYFNQGVSHA VTWKNLKPHI QGIIQDVIFP LMCYTDSDED LWQEDPYEYI RMKFDVFEDF ISPTTAAQTL LFTS CSKRK EVLQKTMGFC YQILTEPAAD PRKKDGALHM IGSLAEILLK KKIYKDQMEF MLQNHVFPLF SSELGYMRAR ACWVL HYFC EVKFKVDQNL QTALELTRRC LIDDREMPVK VEAAIALQVL ISNQEKAKEY IVPFIRPVMQ ALLHIIRETE NDDLTN VIQ KMICEYSEEV TPIAVEMTQH LAMTFNQVIQ TGPDEEGSDD KAVTAMGILN TIDTLLSVVE DHKEITQQLE GICLQVI GT VLQQHVLEFY EEIFSLAHSL TCQQVSPQMW QLLPLVFDIF QQDGFDYFTD MMPLLHNYVT VDTDTLLSDT KYLEMIYS M CKKILTGVAG EDAECHAAKL LEVVILQCKG RGIDQVIPLF VEAALERLTR EVKTSELRTM CLQVAIAALY YSPPLLFNT LENLRFPNNE EPVTNHFIKQ WLNDVDCFLG LHDRKICVLG LCALIELEQR PQVLNQMSSQ ILPAFLLLFN GLKRAYACHA EQENDSDDD GDGEDDEDAA ELGSDEDDID EEGQEYLEIL AKQAGEDGDD EDWEDDDAEE TALEGYTTLL DDEDTPIDEY Q IFKAIFQK LQGRDPVWYQ ALTQGLNEDQ GKQLQDIATL ADQRRAAHES KMIEKHGGYK FNAPVVPSTF NFGNPAPGMN

UniProtKB: Importin 7 L homeolog

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Macromolecule #2: Importin subunit beta-1

MacromoleculeName: Importin subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.257812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARR EVKNYVLQTL GTETYRPSSA SQCVAGIACA EIPVNQWPEL IPQLVANVTN PNSTEHMKES TLEAIGYICQ D IDPEQLQD ...String:
MELITILEKT VSPDRLELEA AQKFLERAAV ENLPTFLVEL SRVLANPGNS QVARVAAGLQ IKNSLTSKDP DIKAQYQQRW LAIDANARR EVKNYVLQTL GTETYRPSSA SQCVAGIACA EIPVNQWPEL IPQLVANVTN PNSTEHMKES TLEAIGYICQ D IDPEQLQD KSNEILTAII QGMRKEEPSN NVKLAATNAL LNSLEFTKAN FDKESERHFI MQVVCEATQC PDTRVRVAAL QN LVKIMSL YYQYMETYMG PALFAITIEA MKSDIDEVAL QGIEFWSNVC DEEMDLAIEA SEAAEQGRPP EHTSKFYAKG ALQ YLVPIL TQTLTKQDEN DDDDDWNPCK AAGVCLMLLA TCCEDDIVPH VLPFIKEHIK NPDWRYRDAA VMAFGCILEG PEPS QLKPL VIQAMPTLIE LMKDPSVVVR DTAAWTVGRI CELLPEAAIN DVYLAPLLQC LIEGLSAEPR VASNVCWAFS SLAEA AYEA ADVADDQEEP ATYCLSSSFE LIVQKLLETT DRPDGHQNNL RSSAYESLME IVKNSAKDCY PAVQKTTLVI MERLQQ VLQ MESHIQSTSD RIQFNDLQSL LCATLQNVLR KVQHQDALQI SDVVMASLLR MFQSTAGSGG VQEDALMAVS TLVEVLG GE FLKYMEAFKP FLGIGLKNYA EYQVCLAAVG LVGDLCRALQ SNIIPFCDEV MQLLLENLGN ENVHRSVKPQ ILSVFGDI A LAIGGEFKKY LEVVLNTLQQ ASQAQVDKSD YDMVDYLNEL RESCLEAYTG IVQGLKGDQE NVHPDVMLVQ PRVEFILSF IDHIAGDEDH TDGVVACAAG LIGDLCTAFG KDVLKLVEAR PMIHELLTEG RRSKTNKAKT LATWATKELR KLKNQA

UniProtKB: Importin subunit beta-1

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Macromolecule #3: Histone H1.0

MacromoleculeName: Histone H1.0 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.927182 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTENSTSAPA AKPKRAKASK KSTDHPKYSD MIVAAIQAEK NRAGSSRQSI QKYIKSHYKV GENADSQIKL SIKRLVTTGV LKQTKGVGA SGSFRLAKSD EPKKSVAFKK TKKEIKKVAT PKKASKPKKA ASKAPTKKPK ATPVKKAKKK LAATPKKAKK P KTVKAKPV ...String:
MTENSTSAPA AKPKRAKASK KSTDHPKYSD MIVAAIQAEK NRAGSSRQSI QKYIKSHYKV GENADSQIKL SIKRLVTTGV LKQTKGVGA SGSFRLAKSD EPKKSVAFKK TKKEIKKVAT PKKASKPKKA ASKAPTKKPK ATPVKKAKKK LAATPKKAKK P KTVKAKPV KASKPKKAKP VKPKAKSSAK RAGKKK

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

BufferpH: 7
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18900
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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