[English] 日本語
Yorodumi
- PDB-9qf0: Cryo-EM structure of the mportin7:Histone H1.0 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qf0
TitleCryo-EM structure of the mportin7:Histone H1.0 complex
Components
  • Histone H1.0
  • Importin 7 L homeolog
KeywordsTRANSPORT PROTEIN / Transport / Importin 7 / Histone 1.0
Function / homology
Function and homology information


positive regulation of transcription regulatory region DNA binding / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / ribosomal protein import into nucleus / chromosome condensation / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / minor groove of adenine-thymine-rich DNA binding / nucleosome binding / transcription repressor complex ...positive regulation of transcription regulatory region DNA binding / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / ribosomal protein import into nucleus / chromosome condensation / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / minor groove of adenine-thymine-rich DNA binding / nucleosome binding / transcription repressor complex / euchromatin / chromatin DNA binding / small GTPase binding / protein import into nucleus / structural constituent of chromatin / nuclear envelope / heterochromatin formation / nucleosome / nucleosome assembly / actin cytoskeleton / double-stranded DNA binding / nuclear body / chromatin / Golgi apparatus / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Importin-11-like, TPR repeats / Exportin-2, central domain / Cse1 / 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-11-like, TPR repeats / Exportin-2, central domain / Cse1 / 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 / 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
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsNeumann, P. / Dickmanns, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Alphafold 3-guided insights into the Importin(beta):Importin7 heterodimer interaction and its binding to histone H1
Authors: Neumann, P.
History
DepositionMar 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Importin 7 L homeolog
C: Histone H1.0


Theoretical massNumber of molelcules
Total (without water)140,4802
Polymers140,4802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Importin 7 L homeolog / MGC52556 protein / RanBP7


Mass: 119553.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Importin7, MGC52556 protei, Xenopus laevis / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: ipo7.L, imp7, ipo7, MGC52556, ranbp7 / Production host: Escherichia coli (E. coli) / References: UniProt: O42480
#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: H1-0, H1F0, H1FV / Production host: Escherichia coli (E. coli) / References: UniProt: P07305
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Binary complex of Importin7:Histone H1.0 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
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
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 40000 nm / Nominal defocus min: 10000 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
9PHENIX1.21_5207model refinement
10RosettaEMrosetta.source.release-371model refinement
CTF correctionType: NONE
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15800 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 7.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039386
ELECTRON MICROSCOPYf_angle_d0.55312720
ELECTRON MICROSCOPYf_dihedral_angle_d5.2441223
ELECTRON MICROSCOPYf_chiral_restr0.0371428
ELECTRON MICROSCOPYf_plane_restr0.0041647

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more