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- EMDB-21487: Arabidopsis thaliana acetohydroxyacid synthase complex with valin... -

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Basic information

Entry
Database: EMDB / ID: EMD-21487
TitleArabidopsis thaliana acetohydroxyacid synthase complex with valine bound
Map data
Sample
  • Complex: Acetohydroxyacid synthase quaternary complex with valine bound
    • Protein or peptide: Acetolactate synthase, chloroplastic
    • Protein or peptide: Acetolactate synthase small subunit 2, chloroplastic
  • Ligand: MAGNESIUM ION
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: THIAMINE DIPHOSPHATE
  • Ligand: VALINE
KeywordsComplex / PLANT PROTEIN
Function / homology
Function and homology information


acetolactate synthase regulator activity / regulation of catalytic activity / acetolactate synthase / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / response to herbicide / chloroplast stroma / chloroplast ...acetolactate synthase regulator activity / regulation of catalytic activity / acetolactate synthase / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / response to herbicide / chloroplast stroma / chloroplast / peroxisome / flavin adenine dinucleotide binding / response to hypoxia / magnesium ion binding
Similarity search - Function
Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / : / AHAS small subunit-like ACT domain / Acetolactate synthase/Transcription factor NikR, C-terminal / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / Thiamine pyrophosphate enzyme ...Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / : / AHAS small subunit-like ACT domain / Acetolactate synthase/Transcription factor NikR, C-terminal / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / ACT domain profile. / ACT domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / ACT-like domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Acetolactate synthase, chloroplastic / Acetolactate synthase small subunit 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsGuddat LW / Low YS
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1087713 Australia
National Health and Medical Research Council (NHMRC, Australia)1147297 Australia
CitationJournal: 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
DepositionFeb 27, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vz8
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21487.png

Downloads & links

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Map

FileDownload / File: emd_21487.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.2
Minimum - Maximum-1.1275145 - 2.134252
Average (Standard dev.)-0.00036394835 (±0.040076617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z419.840419.840419.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.1282.134-0.000

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Supplemental data

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Sample components

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Entire : Acetohydroxyacid synthase quaternary complex with valine bound

EntireName: Acetohydroxyacid synthase quaternary complex with valine bound
Components
  • Complex: Acetohydroxyacid synthase quaternary complex with valine bound
    • Protein or peptide: Acetolactate synthase, chloroplastic
    • Protein or peptide: Acetolactate synthase small subunit 2, chloroplastic
  • Ligand: MAGNESIUM ION
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: THIAMINE DIPHOSPHATE
  • Ligand: VALINE

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Supramolecule #1: Acetohydroxyacid synthase quaternary complex with valine bound

SupramoleculeName: Acetohydroxyacid synthase quaternary complex with valine bound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Recombinant expression from E. coli.
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 720 KDa

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Macromolecule #1: Acetolactate synthase, chloroplastic

MacromoleculeName: Acetolactate synthase, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: acetolactate synthase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 64.025203 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Acetolactate synthase small subunit 2, chloroplastic

MacromoleculeName: Acetolactate synthase small subunit 2, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 53.948906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 8 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #5: THIAMINE DIPHOSPHATE

MacromoleculeName: THIAMINE DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 8 / Formula: TPP
Molecular weightTheoretical: 425.314 Da
Chemical component information

ChemComp-TPP:
THIAMINE DIPHOSPHATE

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Macromolecule #6: VALINE

MacromoleculeName: VALINE / type: ligand / ID: 6 / Number of copies: 8 / Formula: VAL
Molecular weightTheoretical: 117.146 Da
Chemical component information

ChemComp-VAL:
VALINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE
DetailsGlutaraldehyde cross linked

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied 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
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial model
PDB IDChain

5k6q

source_name: PDB, initial_model_type: experimental model

2pc6

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6vz8:
Arabidopsis thaliana acetohydroxyacid synthase complex with valine bound

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