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Yorodumi- 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 | |||||||||||||||
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Title | Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex | |||||||||||||||
Components |
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Keywords | NUCLEAR 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 / protein import into nucleus / structural constituent of chromatin / 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 / protein import into nucleus / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / protein heterodimerization activity / chromatin / protein-containing complex / DNA binding / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | |||||||||||||||
Authors | Bernardes, N.E. / Chook, Y.M. / Fung, H.Y.J. / Chen, Z. / Li, Y. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7unk.cif.gz | 276.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7unk.ent.gz | 214.8 KB | Display | PDB format |
PDBx/mmJSON format | 7unk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7unk_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7unk_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7unk_validation.xml.gz | 47.4 KB | Display | |
Data in CIF | 7unk_validation.cif.gz | 69.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/7unk ftp://data.pdbj.org/pub/pdb/validation_reports/un/7unk | HTTPS FTP |
-Related structure data
Related structure data | 26625MC 8dyoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Nuclear import complex of Imp4-H3-H4-Asf1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.167 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -1000 nm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146050 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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