[English] 日本語
Yorodumi
- EMDB-20700: Arabidopsis thaliana acetohydroxyacid synthase complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20700
TitleArabidopsis thaliana acetohydroxyacid synthase complex
Map dataCryo-EM map of acetohydroxyacid synthase complex from Arabidopsis thaliana
Sample
  • Complex: Acetohydroxyacid synthase quaternary complex
    • Protein or peptide: Acetolactate synthase, chloroplastic
    • Protein or peptide: Acetolactate synthase small subunit 2, chloroplastic
  • Ligand: MAGNESIUM ION
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
  • Ligand: THIAMINE DIPHOSPHATEThiamine pyrophosphate
KeywordsComplex / PLANT PROTEIN
Function / homology
Function and homology information


acetolactate synthase regulator activity / acetolactate synthase activity / acetolactate synthase / regulation of catalytic activity / valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / chloroplast stroma / chloroplast ...acetolactate synthase regulator activity / acetolactate synthase activity / acetolactate synthase / regulation of catalytic activity / valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / chloroplast stroma / chloroplast / peroxisome / : / flavin adenine dinucleotide binding / response to hypoxia / magnesium ion binding
Similarity search - Function
ACT domain / Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / Acetolactate synthase/Transcription factor NikR, C-terminal / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / ACT domain / Thiamine pyrophosphate enzyme ...ACT domain / Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / Acetolactate synthase/Transcription factor NikR, C-terminal / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / ACT 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 / ACT-like domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding 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: 3.8 Å
AuthorsGuddat LW / Low YS / Rao Z
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
DepositionSep 8, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseJul 15, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6u9h
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20700.png

Downloads & links

-
Map

FileDownload / File: emd_20700.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of acetohydroxyacid synthase complex from Arabidopsis thaliana
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.02528372 - 0.046663016
Average (Standard dev.)0.00009721552 (±0.0011338923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0250.0470.000

-
Supplemental data

-
Sample components

-
Entire : Acetohydroxyacid synthase quaternary complex

EntireName: Acetohydroxyacid synthase quaternary complex
Components
  • Complex: Acetohydroxyacid synthase quaternary complex
    • Protein or peptide: Acetolactate synthase, chloroplastic
    • Protein or peptide: Acetolactate synthase small subunit 2, chloroplastic
  • Ligand: MAGNESIUM ION
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
  • Ligand: THIAMINE DIPHOSPHATEThiamine pyrophosphate

-
Supramolecule #1: Acetohydroxyacid synthase quaternary complex

SupramoleculeName: Acetohydroxyacid synthase quaternary complex / 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

-
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 BL21 (bacteria)
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

-
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

-
Macromolecule #3: MAGNESIUM ION

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

-
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 / Flavin adenine dinucleotide

-
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 / Thiamine pyrophosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
GridMaterial: COPPER
VitrificationCryogen name: ETHANE
DetailsGlutaraldehyde cross linked

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Average exposure time: 3.2 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 76

-
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-6u9h:
Arabidopsis thaliana acetohydroxyacid synthase complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more