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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0749 | |||||||||
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Title | 309 K cryoEM structure of Sso-KARI in complex with Mg2+ | |||||||||
![]() | Sso-KARI dodecameric enzyme in complex with Mg2 and cryoEM sample was prepared at 309 K. | |||||||||
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![]() | Complex / ISOMERASE | |||||||||
Function / homology | ![]() ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / isomerase activity / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
![]() | Chen CY / Chang YC / Lin BL / Huang CH / Tsai MD | |||||||||
![]() | ![]() Title: Temperature-Resolved Cryo-EM Uncovers Structural Bases of Temperature-Dependent Enzyme Functions. Authors: Chin-Yu Chen / Yuan-Chih Chang / Bo-Lin Lin / Chun-Hsiang Huang / Ming-Daw Tsai / ![]() Abstract: Protein functions are temperature-dependent, but protein structures are usually solved at a single (often low) temperature because of limitations on the conditions of crystal growth or protein ...Protein functions are temperature-dependent, but protein structures are usually solved at a single (often low) temperature because of limitations on the conditions of crystal growth or protein vitrification. Here we demonstrate the feasibility of solving cryo-EM structures of proteins vitrified at high temperatures, solve 12 structures of an archaeal ketol-acid reductoisomerase (KARI) vitrified at 4-70 °C, and show that structures of both the Mg form (KARI:2Mg) and its ternary complex (KARI:2Mg:NADH:inhibitor) are temperature-dependent in correlation with the temperature dependence of enzyme activity. Furthermore, structural analyses led to dissection of the induced-fit mechanism into ligand-induced and temperature-induced effects and to capture of temperature-resolved intermediates of the temperature-induced conformational change. The results also suggest that it is preferable to solve cryo-EM structures of protein complexes at functional temperatures. These studies should greatly expand the landscapes of protein structure-function relationships and enhance the mechanistic analysis of enzymatic functions. | |||||||||
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 | ![]() | 153.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.2 KB 9.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.5 KB | Display | ![]() |
Images | ![]() | 242.4 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kpkMC ![]() 0740C ![]() 0742C ![]() 0743C ![]() 0746C ![]() 0747C ![]() 0748C ![]() 0750C ![]() 0751C ![]() 0752C ![]() 0753C ![]() 0754C ![]() 6kouC ![]() 6kpaC ![]() 6kpeC ![]() 6kphC ![]() 6kpiC ![]() 6kpjC ![]() 6kq4C ![]() 6kq8C ![]() 6kqjC ![]() 6kqkC ![]() 6kqoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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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Annotation | Sso-KARI dodecameric enzyme in complex with Mg2 and cryoEM sample was prepared at 309 K. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 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 : KARI-Mg2+ complex
Entire | Name: KARI-Mg2+ complex |
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Components |
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-Supramolecule #1: KARI-Mg2+ complex
Supramolecule | Name: KARI-Mg2+ complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Ketol-acid reductoisomerase
Macromolecule | Name: Ketol-acid reductoisomerase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 37.229855 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDKTVLDANL DPLKGKTIGV IGYGNQGRVQ ATIMRENGLN VIVGNVKDKY YELAKKEGFE VYEIDEAVRR SDVALLLIPD EVMKEVYEK KIAPVLQGKK EFVLDFASGY NVAFGLIRPP KSVDTIMVAP RMVGEGIMDL HKQGKGYPVL LGVKQDASGK A WDYAKAIA ...String: MDKTVLDANL DPLKGKTIGV IGYGNQGRVQ ATIMRENGLN VIVGNVKDKY YELAKKEGFE VYEIDEAVRR SDVALLLIPD EVMKEVYEK KIAPVLQGKK EFVLDFASGY NVAFGLIRPP KSVDTIMVAP RMVGEGIMDL HKQGKGYPVL LGVKQDASGK A WDYAKAIA KGIGAIPGGI AVISSFEEEA LLDLMSEHTW VPILFGAIKA CYDIAVKEYG VSPEAALLEF YASGELAEIA RL IAEEGIF NQMVHHSTTS QYGTLTRMFK YYDVVRRIVE NEAKYIWDGS FAKEWSLEQQ AGYPVFYRLW ELATQSEMAK AEK ELYKLL GRKVKND UniProtKB: ketol-acid reductoisomerase |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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: 7.5 |
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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 QUANTUM (4k x 4k) / 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 |