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- PDB-7unk: Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone c... -

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Basic information

Entry
Database: PDB / ID: 7unk
TitleStructure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex
Components
  • Histone H3
  • Histone H4
  • Histone chaperone
  • Importin-4
KeywordsNUCLEAR PROTEIN / Importin / Nuclear Import / Chaperone / Histones / H3 / H4 / ASF1
Function / homology
Function and homology information


DNA replication-dependent chromatin assembly / nucleosome disassembly / nuclear import signal receptor activity / nuclear localization sequence binding / protein localization to nucleus / small GTPase binding / structural constituent of chromatin / protein import into nucleus / nucleosome / nucleosome assembly ...DNA replication-dependent chromatin assembly / nucleosome disassembly / nuclear import signal receptor activity / nuclear localization sequence binding / protein localization to nucleus / small GTPase binding / structural constituent of chromatin / protein import into nucleus / nucleosome / nucleosome assembly / histone binding / protein heterodimerization activity / chromatin / protein-containing complex / DNA binding / membrane / nucleus / cytoplasm
Similarity search - Function
Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Importin beta family / TOG domain / TOG / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain ...Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Importin beta family / TOG domain / TOG / 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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Histone chaperone / Histone H4 / Importin-4 / Histone H3
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsBernardes, N.E. / Chook, Y.M. / Fung, H.Y.J. / Chen, Z. / Li, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141461 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Welch FoundationI-1532 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structure of IMPORTIN-4 bound to the H3-H4-ASF1 histone-histone chaperone complex.
Authors: Natália Elisa Bernardes / Ho Yee Joyce Fung / Yang Li / Zhe Chen / Yuh Min Chook /
Abstract: IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for ...IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for transport cannot be explained by available crystal structures of IMPORTIN-4-histone tail peptide complexes. Our 3.5-Å IMPORTIN-4-H3-H4-ASF1 cryoelectron microscopy structure reveals the full nuclear import complex and shows a binding mode different from suggested by previous structures. The N-terminal half of IMPORTIN-4 clamps the globular H3-H4 domain and H3 αN helix, while its C-terminal half binds the H3 N-terminal tail weakly; tail contribution to binding energy is negligible. ASF1 binds H3-H4 without contacting IMPORTIN-4. Together, ASF1 and IMPORTIN-4 shield nucleosomal H3-H4 surfaces to chaperone and import it into the nucleus where RanGTP binds IMPORTIN-4, causing large conformational changes to release H3-H4-ASF1. This work explains how full-length H3-H4 binds IMPORTIN-4 in the cytoplasm and how it is released in the nucleus.
History
DepositionApr 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin-4
C: Histone H3
D: Histone chaperone
E: Histone H4


Theoretical massNumber of molelcules
Total (without water)177,2634
Polymers177,2634
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Importin-4 / Imp4 / Importin-4b / Imp4b / Ran-binding protein 4 / RanBP4


Mass: 118832.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPO4, IMP4B, RANBP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TEX9
#2: Protein Histone H3


Mass: 15407.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h3g, h3c8, H3l / Production host: Escherichia coli (E. coli) / References: UniProt: Q92133
#3: Protein Histone chaperone / Asf1


Mass: 31629.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ASF1, GI527_G0003133 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L0YDQ7
#4: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Nuclear import complex of Imp4-H3-H4-Asf1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.167 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -1000 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146050 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311216
ELECTRON MICROSCOPYf_angle_d0.60215228
ELECTRON MICROSCOPYf_dihedral_angle_d5.7921541
ELECTRON MICROSCOPYf_chiral_restr0.041783
ELECTRON MICROSCOPYf_plane_restr0.0061985

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