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Yorodumi- EMDB-21487: Arabidopsis thaliana acetohydroxyacid synthase complex with valin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21487 | |||||||||
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Title | Arabidopsis thaliana acetohydroxyacid synthase complex with valine bound | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / PLANT PROTEIN | |||||||||
Function / homology | Function and homology information acetolactate synthase regulator activity / acetolactate synthase / acetolactate synthase complex / acetolactate synthase activity / regulation of catalytic activity / valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / chloroplast stroma ...acetolactate synthase regulator activity / acetolactate synthase / acetolactate synthase complex / acetolactate synthase activity / regulation of catalytic activity / valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / chloroplast stroma / amino acid biosynthetic process / chloroplast / peroxisome / : / flavin adenine dinucleotide binding / response to hypoxia / magnesium ion binding / mitochondrion / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.45 Å | |||||||||
Authors | Guddat LW / Low YS | |||||||||
Funding support | Australia, 2 items
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Citation | Journal: Nature / Year: 2020 Title: Structures of fungal and plant acetohydroxyacid synthases. Authors: Thierry Lonhienne / Yu Shang Low / Mario D Garcia / Tristan Croll / Yan Gao / Quan Wang / Lou Brillault / Craig M Williams / James A Fraser / Ross P McGeary / Nicholas P West / Michael J ...Authors: Thierry Lonhienne / Yu Shang Low / Mario D Garcia / Tristan Croll / Yan Gao / Quan Wang / Lou Brillault / Craig M Williams / James A Fraser / Ross P McGeary / Nicholas P West / Michael J Landsberg / Zihe Rao / Gerhard Schenk / Luke W Guddat / Abstract: Acetohydroxyacid synthase (AHAS), also known as acetolactate synthase, is a flavin adenine dinucleotide-, thiamine diphosphate- and magnesium-dependent enzyme that catalyses the first step in the ...Acetohydroxyacid synthase (AHAS), also known as acetolactate synthase, is a flavin adenine dinucleotide-, thiamine diphosphate- and magnesium-dependent enzyme that catalyses the first step in the biosynthesis of branched-chain amino acids. It is the target for more than 50 commercial herbicides. AHAS requires both catalytic and regulatory subunits for maximal activity and functionality. Here we describe structures of the hexadecameric AHAS complexes of Saccharomyces cerevisiae and dodecameric AHAS complexes of Arabidopsis thaliana. We found that the regulatory subunits of these AHAS complexes form a core to which the catalytic subunit dimers are attached, adopting the shape of a Maltese cross. The structures show how the catalytic and regulatory subunits communicate with each other to provide a pathway for activation and for feedback inhibition by branched-chain amino acids. We also show that the AHAS complex of Mycobacterium tuberculosis adopts a similar structure, thus demonstrating that the overall AHAS architecture is conserved across kingdoms. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21487.map.gz | 483.3 MB | EMDB map data format | |
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Header (meta data) | emd-21487-v30.xml emd-21487.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_21487.png | 84.7 KB | ||
Filedesc metadata | emd-21487.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21487 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21487 | HTTPS FTP |
-Related structure data
Related structure data | 6vz8MC 6u9dC 6u9hC 6wo1C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21487.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Acetohydroxyacid synthase quaternary complex with valine bound
Entire | Name: Acetohydroxyacid synthase quaternary complex with valine bound |
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Components |
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-Supramolecule #1: Acetohydroxyacid synthase quaternary complex with valine bound
Supramolecule | Name: Acetohydroxyacid synthase quaternary complex with valine bound type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Recombinant expression from E. coli. |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 720 KDa |
-Macromolecule #1: Acetolactate synthase, chloroplastic
Macromolecule | Name: Acetolactate synthase, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: acetolactate synthase |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 64.025203 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTFISRFAPD QPRKGADILV EALERQGVET VFAYPGGASM EIHQALTRSS SIRNVLPRHE QGGVFAAEGY ARSSGKPGIC IATSGPGAT NLVSGLADAL LDSVPLVAIT GQVPRRMIGT DAFQETPIVE VTRSITKHNY LVMDVEDIPR IIEEAFFLAT S GRPGPVLV ...String: MTFISRFAPD QPRKGADILV EALERQGVET VFAYPGGASM EIHQALTRSS SIRNVLPRHE QGGVFAAEGY ARSSGKPGIC IATSGPGAT NLVSGLADAL LDSVPLVAIT GQVPRRMIGT DAFQETPIVE VTRSITKHNY LVMDVEDIPR IIEEAFFLAT S GRPGPVLV DVPKDIQQQL AIPNWEQAMR LPGYMSRMPK PPEDSHLEQI VRLISESKKP VLYVGGGCLN SSDELGRFVE LT GIPVAST LMGLGSYPCD DELSLHMLGM HGTVYANYAV EHSDLLLAFG VRFDDRVTGK LEAFASRAKI VHIDIDSAEI GKN KTPHVS VCGDVKLALQ GMNKVLENRA EELKLDFGVW RNELNVQKQK FPLSFKTFGE AIPPQYAIKV LDELTDGKAI ISTG VGQHQ MWAAQFYNYK KPRQWLSSGG LGAMGFGLPA AIGASVANPD AIVVDIDGDG SFIMNVQELA TIRVENLPVK VLLLN NQHL GMVMQWEDRF YKANRAHTFL GDPAQEDEIF PNMLLFAAAC GIPAARVTKK ADLREAIQTM LDTPGPYLLD VICPHQ EHV LPMIPSGGTF NDVITEGDGR IKY UniProtKB: Acetolactate synthase, chloroplastic |
-Macromolecule #2: Acetolactate synthase small subunit 2, chloroplastic
Macromolecule | Name: Acetolactate synthase small subunit 2, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 53.948906 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAAISVSSSP SIRCLRSACS DSSPALVSST RVSFPAKISY LSGISSHRGD EMGKRMEGFV RSVDGKISDA SFSEASSATP KSKVRKHTI SVFVGDESGM INRIAGVFAR RGYNIESLAV GLNRDKALFT IVVCGTERVL QQVIEQLQKL VNVLKVEDIS S EPQVEREL ...String: MAAISVSSSP SIRCLRSACS DSSPALVSST RVSFPAKISY LSGISSHRGD EMGKRMEGFV RSVDGKISDA SFSEASSATP KSKVRKHTI SVFVGDESGM INRIAGVFAR RGYNIESLAV GLNRDKALFT IVVCGTERVL QQVIEQLQKL VNVLKVEDIS S EPQVEREL MLVKVNAHPE SRAEIMWLVD TFRARVVDIA EHALTIEVTG DPGKMIAVER NLKKFQIREI VRTGKIALRR EK MGATAPF WRFSAASYPD LKEQAPVSVL RSSKKGAIVP QKETSAGGDV YPVEPFFDPK VHRILDAHWG LLTDEDTSGL RSH TLSLLV NDIPGVLNIV TGVFARRGYN IQSLAVGHAE TKGISRITTV IPATDESVSK LVQQLYKLVD VHEVHDLTHL PFSE RELML IKIAVNAAAR RDVLDIASIF RAKAVDVSDH TITLQLTGDL DKMVALQRLL EPYGICEVAR TGRVALARES GVDSK YLRG YSFPLTG UniProtKB: Acetolactate synthase small subunit 1, chloroplastic |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 8 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Macromolecule #5: THIAMINE DIPHOSPHATE
Macromolecule | Name: THIAMINE DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 8 / Formula: TPP |
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Molecular weight | Theoretical: 425.314 Da |
Chemical component information | ChemComp-TPP: |
-Macromolecule #6: VALINE
Macromolecule | Name: VALINE / type: ligand / ID: 6 / Number of copies: 8 / Formula: VAL |
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Molecular weight | Theoretical: 117.146 Da |
Chemical component information | ChemComp-VAL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
Details | Glutaraldehyde cross linked |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Average exposure time: 3.2 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 290516 |