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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24326 | |||||||||||||||
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Title | Methanococcus maripaludis chaperonin, open conformation 2 | |||||||||||||||
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![]() | Open conformation / CHAPERONE | |||||||||||||||
Function / homology | ![]() chaperonin-containing T-complex / ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.4 Å | |||||||||||||||
![]() | Zhao Y / Schmid M | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin. Authors: Yanyan Zhao / Michael F Schmid / Judith Frydman / Wah Chiu / ![]() Abstract: Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism ...Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.5 KB 11.5 KB | Display Display | ![]() |
Images | ![]() | 33.5 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r9iMC ![]() 7r9eC ![]() 7r9hC ![]() 7r9jC ![]() 7r9kC ![]() 7r9mC ![]() 7r9oC ![]() 7r9uC ![]() 7rakC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 48.4 Data #1: aligned particle image [picked particles - single frame - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : MmCpn
Entire | Name: MmCpn |
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Components |
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-Supramolecule #1: MmCpn
Supramolecule | Name: MmCpn / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1 MDa |
-Macromolecule #1: Chaperonin
Macromolecule | Name: Chaperonin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 54.372539 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: RDAQRMNILA GRIIAETVRS TLGPKGMDKM LVDDLGDVVV TNDGVTILRE MSVEHPAAKM LIEVAKTQEK EVGDGTTTAV VVAGELLRK AEELLDQNVH PTIVVKGYQA AAQKAQELLK TIACEVGAQD KEILTKIAMT SITGKGAEKA KEKLAEIIVE A VSAVVDDE ...String: RDAQRMNILA GRIIAETVRS TLGPKGMDKM LVDDLGDVVV TNDGVTILRE MSVEHPAAKM LIEVAKTQEK EVGDGTTTAV VVAGELLRK AEELLDQNVH PTIVVKGYQA AAQKAQELLK TIACEVGAQD KEILTKIAMT SITGKGAEKA KEKLAEIIVE A VSAVVDDE GKVDKDLIKI EKKSGASIDD TELIKGVLVD KERVSAQMPK KVTDAKIALL NCAIEIKETE TDAEIRITDP AK LMEFIEQ EEKMLKDMVA EIKASGANVL FCQKGIDDLA QHYLAKEGIV AARRVKKSDM EKLAKATGAN VITNIKDLSA QDL GDAGLV EERKISGDSM IFVEECKHPK AVTMLIRGTT EHVIEEVARA VDDAVGVVGC TIEDGRIVSG GGSTEVELSM KLRE YAEGI SGREQLAVRA FADALEVIPR TLAENAGLDA IEILVKVRAA HASNGNKCAG LNVFTGAVED MCENGVVEPL RVKTQ AIQS AAESTEMLLR IDDVIAAEKL R UniProtKB: Chaperonin |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3200 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-7r9i: |