+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40955 | |||||||||
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Title | Cryo-EM structure of dodecameric hub domain of CaMKII alpha | |||||||||
Map data | Dodecameric CaMKII alpha hub | |||||||||
Sample |
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Keywords | High-order oligomer / Protein Kinase / Signaling / Memory / SIGNALING PROTEIN | |||||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / : / Green fluorescent protein Function and homology information | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Chien C-T / Chiu W / Khan S | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Commun Biol / Year: 2024 Title: Hub stability in the calcium calmodulin-dependent protein kinase II. Authors: Chih-Ta Chien / Henry Puhl / Steven S Vogel / Justin E Molloy / Wah Chiu / Shahid Khan / Abstract: The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within ...The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40955.map.gz | 203.4 MB | EMDB map data format | |
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Header (meta data) | emd-40955-v30.xml emd-40955.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_40955.png | 62.6 KB | ||
Filedesc metadata | emd-40955.cif.gz | 5.5 KB | ||
Others | emd_40955_half_map_1.map.gz emd_40955_half_map_2.map.gz | 200.1 MB 200.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40955 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40955 | HTTPS FTP |
-Validation report
Summary document | emd_40955_validation.pdf.gz | 804.8 KB | Display | EMDB validaton report |
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Full document | emd_40955_full_validation.pdf.gz | 804.4 KB | Display | |
Data in XML | emd_40955_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_40955_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40955 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40955 | HTTPS FTP |
-Related structure data
Related structure data | 8t15MC 8sygC 8t17C 8t18C 8t6kC 8t6qC 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_40955.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Dodecameric CaMKII alpha hub | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.741 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40955_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40955_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Venus-tagged CaMKII Alpha Association Domain
Entire | Name: Venus-tagged CaMKII Alpha Association Domain |
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Components |
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-Supramolecule #1: Venus-tagged CaMKII Alpha Association Domain
Supramolecule | Name: Venus-tagged CaMKII Alpha Association Domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-Macromolecule #1: Venus-tagged CaMKII Alpha Association Domain
Macromolecule | Name: Venus-tagged CaMKII Alpha Association Domain / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: Ca2+/calmodulin-dependent protein kinase |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 45.877539 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH VSKGEELFTG VVPILVELDG DVNGHKFSVS GEGEGDATYG KLTLKLICTT GKLPVPWPTL VTTLGYGLQ CFARYPDHMK QHDFFKSAMP EGYVQERTIF FKDDGNYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH K LEYNYNSH ...String: MGSSHHHHHH SSGLVPRGSH VSKGEELFTG VVPILVELDG DVNGHKFSVS GEGEGDATYG KLTLKLICTT GKLPVPWPTL VTTLGYGLQ CFARYPDHMK QHDFFKSAMP EGYVQERTIF FKDDGNYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH K LEYNYNSH NVYITADKQK NGIKANFKIR HNIEDGGVQL ADHYQQNTPI GDGPVLLPDN HYLSYQSKLS KDPNEKRDHM VL LEFVTAA GITLGMDELY KSGLRSRAQA SNSAVDVRKQ EIIKVTEQLI EAISNGDFES YTKMCDPGMT AFEPEALGNL VEG LDFHRF YFENLWSRNS KPVHTTILNP HIHLMGDESA CIAYIRITQY LDAGGIPRTA QSEETRVWHR RDGKWQIVHF HRSG APSVL PH UniProtKB: Green fluorescent protein, UNIPROTKB: P11275 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 20 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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: 1.5 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94506 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |