+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28796 | |||||||||
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Title | Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 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 / Postmitotic nuclear pore complex (NPC) reformation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones ...regulation of cell cycle phase transition / HATs acetylate histones / Postmitotic nuclear pore complex (NPC) reformation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / 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 / replication fork protection complex / Oxidative Stress Induced Senescence / 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 / mRNA transport / Ub-specific processing proteases / ribosomal subunit export from nucleus / nuclear pore / nucleosomal DNA binding / heterochromatin formation / small GTPase binding / protein import into nucleus / structural constituent of chromatin / 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 | single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||
Authors | Jiou J / Chook YM | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28796.map.gz | 62.4 MB | EMDB map data format | |
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Header (meta data) | emd-28796-v30.xml emd-28796.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
Images | emd_28796.png | 78.7 KB | ||
Filedesc metadata | emd-28796.cif.gz | 6.6 KB | ||
Others | emd_28796_half_map_1.map.gz emd_28796_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28796 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28796 | HTTPS FTP |
-Related structure data
Related structure data | 8f1eMC 8f0xC 8f19C 8f7aC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28796.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half-A
File | emd_28796_half_map_1.map | ||||||||||||
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Annotation | half-A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28796_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B
Entire | Name: Complex of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B |
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Components |
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-Supramolecule #1: Complex of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B
Supramolecule | Name: Complex of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
-Macromolecule #1: Importin subunit beta-5
Macromolecule | Name: Importin subunit beta-5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 114.019695 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MDINELIIGA QSADKHTREV AETQLLQWCD SDASQVFKAL ANVALQHEAS LESRQFALLS LRKLITMYWS PGFESYRSTS NVEIDVKDF IREVLLKLCL NDNENTKIKN GASYCIVQIS AVDFPDQWPQ LLTVIYDAIS HQHSLNAMSL LNEIYDDVVS E EMFFEGGI ...String: MDINELIIGA QSADKHTREV AETQLLQWCD SDASQVFKAL ANVALQHEAS LESRQFALLS LRKLITMYWS PGFESYRSTS NVEIDVKDF IREVLLKLCL NDNENTKIKN GASYCIVQIS AVDFPDQWPQ LLTVIYDAIS HQHSLNAMSL LNEIYDDVVS E EMFFEGGI GLATMEIVFK VLNTETSTLI AKIAALKLLK ACLLQMSSHN EYDEASRKSF VSQCLATSLQ ILGQLLTLNF GN VDVISQL KFKSIIYENL VFIKNDFSRK HFSSELQKQF KIMAIQDLEN VTHINANVET TESEPLLETV HDCSIYIVEF LTS VCTLQF SVEEMNKIIT SLTILCQLSS ETREIWTSDF NTFVSKETGL AASYNVRDQA NEFFTSLPNP QLSLIFKVVS NDIE HSTCN YSTLESLLYL LQCILLNDDE ITGENIDQSL QILIKTLENI LVSQEIPELI LARAILTIPR VLDKFIDALP DIKPL TSAF LAKSLNLALK SDKELIKSAT LIAFTYYCYF AELDSVLGPE VCSETQEKVI RIINQVSSDA EEDTNGALME VLSQVI SYN PKEPHSRKEI LQAEFHLVFT ISSEDPANVQ VVVQSQECLE KLLDNINMDN YKNYIELCLP SFINVLDSNN ANNYRYS PL LSLVLEFITV FLKKKPNDGF LPDEINQYLF EPLAKVLAFS TEDETLQLAT EAFSYLIFNT DTRAMEPRLM DIMKVLER L LSLEVSDSAA MNVGPLVVAI FTRFSKEIQP LIGRILEAVV VRLIKTQNIS TEQNLLSVLC FLTCNDPKQT VDFLSSFQI DNTDALTLVM RKWIEAFEVI RGEKRIKENI VALSNLFFLN DKRLQKVVVN GNLIPYEGDL IITRSMAKKM PDRYVQVPLY TKIIKLFVS ELSFQSKQPN PEQLITSDIK QEVVNANKDD DNDDWEDVDD VLDYDKLKEY IDDDVDEEAD DDSDDITGLM D VKESVVQL LVRFFKEVAS KDVSGFHCIY ETLSDSERKV LSEALL UniProtKB: Importin subunit beta-5 |
-Macromolecule #2: Histone H2A.2
Macromolecule | Name: Histone H2A.2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 13.88198 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGGKGGKAGS AAKASQSRSA KAGLTFPVGR VHRLLRRGNY AQRIGSGAPV YLTAVLEYLA AEILELAGNA ARDNKKTRII PRHLQLAIR NDDELNKLLG NVTIAQGGVL PNIHQNLLPK KSAKTAKASQ EL UniProtKB: Histone H2A.2 |
-Macromolecule #3: Histone H2B.2
Macromolecule | Name: Histone H2B.2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 14.133145 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SSAAEKKPAS KAPAEKKPAA KKTSTSVDGK KRSKVRKETY SSYIYKVLKQ THPDTGISQK SMSILNSFVN DIFERIATEA SKLAAYNKK STISAREIQT AVRLILPGEL AKHAVSEGTR AVTKYSSSTQ A UniProtKB: Histone H2B.2 |
-Macromolecule #4: GTP-binding nuclear protein GSP1/CNR1
Macromolecule | Name: GTP-binding nuclear protein GSP1/CNR1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 20.41759 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MSAPAANGEV PTFKLVLVGD GGTGKTTFVK RHLTGEFEKK YIATIGVEVH PLSFYTNFGE IKFDVWDTAG LEKFGGLRDG YYINAQCAI IMFDVTSRIT YKNVPNWHRD LVRVCENIPI VLCGNKVDVK ERKVKAKTIT FHRKKNLQYY DISAKSNYNF E KPFLWLAR KLAGNPQLEF V UniProtKB: GTP-binding nuclear protein GSP1/CNR1 |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134915 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |