+Open data
-Basic information
Entry | Database: PDB / ID: 8f1e | ||||||
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Title | Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/STRUCTURAL PROTEIN/NUCLEAR PROTEIN / Karyopherin Beta / Nuclear Transport / GTPase / Histone Chaperone / Histones / PROTEIN TRANSPORT-STRUCTURAL PROTEIN-NUCLEAR PROTEIN complex | ||||||
Function / homology | Function and homology information regulation of cell cycle phase transition / HATs acetylate histones / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / Postmitotic nuclear pore complex (NPC) reformation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of nucleocytoplasmic transport / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones ...regulation of cell cycle phase transition / HATs acetylate histones / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / Postmitotic nuclear pore complex (NPC) reformation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of nucleocytoplasmic transport / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / replication fork protection complex / RMTs methylate histone arginines / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / NLS-bearing protein import into nucleus / nucleus organization / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / heterochromatin organization / Ub-specific processing proteases / mRNA transport / nucleosomal DNA binding / ribosomal subunit export from nucleus / nuclear pore / small GTPase binding / structural constituent of chromatin / protein import into nucleus / nucleosome / nuclear envelope / chromatin organization / protein heterodimerization activity / DNA repair / GTPase activity / regulation of DNA-templated transcription / GTP binding / DNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å | ||||||
Authors | Jiou, J. / Chook, Y.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Mechanism of RanGTP priming H2A-H2B release from Kap114 in an atypical RanGTP•Kap114•H2A-H2B complex. Authors: Jenny Jiou / Joy M Shaffer / Natalia E Bernades / Ho Yee Joyce Fung / Juliana Kikumoto Dias / Sheena D'Arcy / Yuh Min Chook / Abstract: Previously, we showed that the nuclear import receptor Importin-9 wraps around the H2A-H2B core to chaperone and transport it from the cytoplasm to the nucleus. However, unlike most nuclear import ...Previously, we showed that the nuclear import receptor Importin-9 wraps around the H2A-H2B core to chaperone and transport it from the cytoplasm to the nucleus. However, unlike most nuclear import systems where RanGTP dissociates cargoes from their importins, RanGTP binds stably to the Importin-9•H2A-H2B complex, and formation of the ternary RanGTP•Importin-9•H2A-H2B complex facilitates H2A-H2B release to the assembling nucleosome. It was unclear how RanGTP and the cargo H2A-H2B can bind simultaneously to an importin, and how interactions of the three components position H2A-H2B for release. Here, we show cryo-EM structures of Importin-9•RanGTP and of its yeast homolog Kap114, including Kap114•RanGTP, Kap114•H2A-H2B, and RanGTP•Kap114•H2A-H2B, to explain how the conserved Kap114 binds H2A-H2B and RanGTP simultaneously and how the GTPase primes histone transfer to the nucleosome. In the ternary complex, RanGTP binds to the N-terminal repeats of Kap114 in the same manner as in the Kap114/Importin-9•RanGTP complex, and H2A-H2B binds via its acidic patch to the Kap114 C-terminal repeats much like in the Kap114/Importin-9•H2A-H2B complex. Ran binds to a different conformation of Kap114 in the ternary RanGTP•Kap114•H2A-H2B complex. Here, Kap114 no longer contacts the H2A-H2B surface proximal to the H2A docking domain that drives nucleosome assembly, positioning it for transfer to the assembling nucleosome or to dedicated H2A-H2B chaperones 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 | 8f1e.cif.gz | 263 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f1e.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8f1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/8f1e ftp://data.pdbj.org/pub/pdb/validation_reports/f1/8f1e | HTTPS FTP |
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-Related structure data
Related structure data | 28796MC 8f0xC 8f19C 8f7aC 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
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 114019.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: KAP114, YGL241W, HRC1004 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P53067 |
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#2: Protein | Mass: 13881.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: HTA2, H2A2, YBL003C, YBL0103 / Production host: Escherichia coli (E. coli) / References: UniProt: P04912 |
#3: Protein | Mass: 14133.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: HTB2, H2B2, YBL002W, YBL0104 / Production host: Escherichia coli (E. coli) / References: UniProt: P02294 |
#4: Protein | Mass: 20417.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: GSP1, CNR1, CST17, YLR293C, L8003.19 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P32835 |
-Non-polymers , 2 types, 2 molecules
#5: Chemical | ChemComp-MG / |
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#6: Chemical | ChemComp-GTP / |
-Details
Has ligand of interest | Y |
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-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: Complex of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
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 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 4 K |
-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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134915 / Symmetry type: POINT | ||||||||||||||||||||||||
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