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- EMDB-10105: Structure of Azospirillum brasilense Glutamate Synthase in a4b3 o... -

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Basic information

Entry
Database: EMDB / ID: EMD-10105
TitleStructure of Azospirillum brasilense Glutamate Synthase in a4b3 oligomeric state
Map dataPostprocessed final 3D reconstruction of GltS a4b3 oligomeric assembly.
Sample
  • Complex: Glutamate Synthase complex in a4b3 oligomeric state
    • Protein or peptide: Glutamate synthase [NADPH] large chain
    • Protein or peptide: Glutamate synthase [NADPH] small chain
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FE3-S4 CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
Function / homology
Function and homology information


glutamate synthase (NADPH) / glutamate synthase (NADPH) activity / L-glutamate biosynthetic process / 3 iron, 4 sulfur cluster binding / glutamine metabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Glutamate synthase NADPH small chain-like / : / Glutamate synthase domain / Glutamate synthase, central-N / Glutamine amidotransferases class-II / Conserved region in glutamate synthase / Glutamate synthase central domain / Glutamate synthase, alpha subunit, C-terminal / : / GXGXG motif ...Glutamate synthase NADPH small chain-like / : / Glutamate synthase domain / Glutamate synthase, central-N / Glutamine amidotransferases class-II / Conserved region in glutamate synthase / Glutamate synthase central domain / Glutamate synthase, alpha subunit, C-terminal / : / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Alpha-helical ferredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Nucleophile aminohydrolases, N-terminal / FAD/NAD(P)-binding domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
Glutamate synthase [NADPH] large chain / Glutamate synthase [NADPH] small chain
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsSwuec P
CitationJournal: J Mol Biol / Year: 2019
Title: Cryo-EM Structures of Azospirillum brasilense Glutamate Synthase in Its Oligomeric Assemblies.
Authors: Paolo Swuec / Antonio Chaves-Sanjuan / Carlo Camilloni / Maria Antonietta Vanoni / Martino Bolognesi /
Abstract: Bacterial NADPH-dependent glutamate synthase (GltS) is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate. GltS functional ...Bacterial NADPH-dependent glutamate synthase (GltS) is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate. GltS functional unit hosts an α-subunit (αGltS) and a β-subunit (βGltS) that assemble in different αβ oligomers in solution. Here, we present the cryo-electron microscopy structures of Azospirillum brasilense GltS in four different oligomeric states (αβ, αβ, αβ and αβ, in the 3.5- to 4.1-Å resolution range). Our study provides a comprehensive GltS model that details the inter-protomeric assemblies and allows unequivocal location of the FAD cofactor and of two electron transfer [4Fe-4S] clusters within βGltS.
History
DepositionJul 3, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseSep 11, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s6t
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10105.png

Downloads & links

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Map

FileDownload / File: emd_10105.map.gz / Format: CCP4 / Size: 111.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed final 3D reconstruction of GltS a4b3 oligomeric assembly.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 308 pix.
= 439.208 Å		1.43 Å/pix.
x 308 pix.
= 439.208 Å		1.43 Å/pix.
x 308 pix.
= 439.208 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.426 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.16051036 - 0.6018364
Average (Standard dev.)0.00007343924 (±0.017750837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions308308308
Spacing308308308
CellA=B=C: 439.208 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4261.4261.426
M x/y/z308308308
origin x/y/z0.0000.0000.000
length x/y/z439.208439.208439.208
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS308308308
D min/max/mean-0.1610.6020.000

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Supplemental data

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Mask #1

Fileemd_10105_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened final 3D reconstruction of GltS a4b3 oligomeric assembly.

Fileemd_10105_additional.map
AnnotationUnsharpened final 3D reconstruction of GltS a4b3 oligomeric assembly.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half-map 1 for 3D reconstruction of GltS...

Fileemd_10105_half_map_1.map
AnnotationUnsharpened half-map 1 for 3D reconstruction of GltS a4b3 oligomeric assembly.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half-map 2 for 3D reconstruction of GltS...

Fileemd_10105_half_map_2.map
AnnotationUnsharpened half-map 2 for 3D reconstruction of GltS a4b3 oligomeric assembly.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Glutamate Synthase complex in a4b3 oligomeric state

EntireName: Glutamate Synthase complex in a4b3 oligomeric state
Components
  • Complex: Glutamate Synthase complex in a4b3 oligomeric state
    • Protein or peptide: Glutamate synthase [NADPH] large chain
    • Protein or peptide: Glutamate synthase [NADPH] small chain
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FE3-S4 CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Glutamate Synthase complex in a4b3 oligomeric state

SupramoleculeName: Glutamate Synthase complex in a4b3 oligomeric state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Azospirillum brasilense (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Glutamate synthase [NADPH] large chain

MacromoleculeName: Glutamate synthase [NADPH] large chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: glutamate synthase (NADPH)
Source (natural)Organism: Azospirillum brasilense (bacteria)
Molecular weightTheoretical: 166.224734 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTELNQGEQ FVADFRANAA ALTTANAYNP EDEHDACGVG FIAAIDGKPR RSVVEKGIEA LKAVWHRGAV DADGKTGDGA GIHVAVPQK FFKDHVKVIG HRAPDNKLAV GQVFLPRISL DAQEACRCIV ETEILAFGYY IYGWRQVPIN VDIIGEKANA T RPEIEQII ...String:
MTTELNQGEQ FVADFRANAA ALTTANAYNP EDEHDACGVG FIAAIDGKPR RSVVEKGIEA LKAVWHRGAV DADGKTGDGA GIHVAVPQK FFKDHVKVIG HRAPDNKLAV GQVFLPRISL DAQEACRCIV ETEILAFGYY IYGWRQVPIN VDIIGEKANA T RPEIEQII VGNNKGVSDE QFELDLYIIR RRIEKAVKGE QINDFYICSL SARSIIYKGM FLAEQLTTFY PDLLDERFES DF AIYHQRY STNTFPTWPL AQPFRMLAHN GEINTVKGNV NWMKAHETRM EHPAFGTHMQ DLKPVIGVGL SDSGSLDTVF EVM VRAGRT APMVKMMLVP QALTSSQTTP DNHKALIQYC NSVMEPWDGP AALAMTDGRW VVGGMDRNGL RPMRYTITTD GLII GGSET GMVKIDETQV IEKGRLGPGE MIAVDLQSGK LYRDRELKDH LATLKPWDKW VQNTTHLDEL VKTASLKGEP SDMDK AELR RRQQAFGLTM EDMELILHPM VEDGKEAIGS MGDDSPIAVL SDKYRGLHHF FRQNFSQVTN PPIDSLRERR VMSLKT RLG NLGNILDEDE TQTRLLQLES PVLTTAEFRA MRDYMGDTAA EIDATFPVDG GPEALRDALR RIRQETEDAV RGGATHV IL TDEAMGPARA AIPAILATGA VHTHLIRSNL RTFTSLNVRT AEGLDTHYFA VLIGVGATTV NAYLAQEAIA ERHRRGLF G SMPLEKGMAN YKKAIDDGLL KIMSKMGISV ISSYRGGGNF EAIGLSRALV AEHFPAMVSR ISGIGLNGIQ KKVLEQHAT AYNEEVVALP VGGFYRFRKS GDRHGWEGGV IHTLQQAVTN DSYTTFKKYS EQVNKRPPMQ LRDLLELRST KAPVPVDEVE SITAIRKRF ITPGMSMGAL SPEAHGTLNV AMNRIGAKSD SGEGGEDPAR FRPDKNGDNW NSAIKQVASG RFGVTAEYLN Q CRELEIKV AQGAKPGEGG QLPGFKVTEM IARLRHSTPG VMLISPPPHH DIYSIEDLAQ LIYDLKQINP DAKVTVKLVS RS GIGTIAA GVAKANADII LISGNSGGTG ASPQTSIKFA GLPWEMGLSE VHQVLTLNRL RHRVRLRTDG GLKTGRDIVI AAM LGAEEF GIGTASLIAM GCIMVRQCHS NTCPVGVCVQ DDKLRQKFVG TPEKVVNLFT FLAEEVREIL AGLGFRSLNE VIGR TDLLH QVSRGAEHLD DLDLNPRLAQ VDPGENARYC TLQGRNEVPD TLDARIVADA RPLFEEGEKM QLAYNARNTQ RAIGT RLSS MVTRKFGMFG LQPGHITIRL RGTAGQSLGA FAVQGIKLEV MGDANDYVGK GLSGGTIVVR PTTSSPLETN KNTIIG NTV LYGATAGKLF AAGQAGERFA VRNSGATVVV EGCGSNGCEY MTGGTAVILG RVGDNFAAGM TGGMAYVYDL DDSLPLY IN DESVIFQRIE VGHYESQLKH LIEEHVTETQ SRFAAEILND WAREVTKFWQ VVPKEMLNRL EVPVHLPKAI SAE

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Macromolecule #2: Glutamate synthase [NADPH] small chain

MacromoleculeName: Glutamate synthase [NADPH] small chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: glutamate synthase (NADPH)
Source (natural)Organism: Azospirillum brasilense (bacteria)
Molecular weightTheoretical: 52.425109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANQRMLGFV HTAQRMPDKR PAAERRQDFA EIYARFSDER ANEQANRCSQ CGVPFCQVHC PVSNNIPDWL KLTSEGRLEE AYEVSQATN NFPEICGRIC PQDRLCEGNC VIEQSTHGAV TIGSVEKYIN DTAWDQGWVK PRTPSRELGL SVGVIGAGPA G LAAAEELR ...String:
MANQRMLGFV HTAQRMPDKR PAAERRQDFA EIYARFSDER ANEQANRCSQ CGVPFCQVHC PVSNNIPDWL KLTSEGRLEE AYEVSQATN NFPEICGRIC PQDRLCEGNC VIEQSTHGAV TIGSVEKYIN DTAWDQGWVK PRTPSRELGL SVGVIGAGPA G LAAAEELR AKGYEVHVYD RYDRMGGLLV YGIPGFKLEK SVVERRVKLL ADAGVIYHPN FEVGRDASLP ELRRKHVAVL VA TGVYKAR DIKAPGSGLG NIVAALDYLT TSNKVSLGDT VEAYENGSLN AAGKHVVVLG GGDTAMDCVR TAIRQGATSV KCL YRRDRK NMPGSQREVA HAEEEGVEFI WQAAPEGFTG DTVVTGVRAV RIHLGVADAT GRQTPQVIEG SEFTVQADLV IKAL GFEPE DLPNAFDEPE LKVTRWGTLL VDHRTKMTNM DGVFAAGDIV RGASLVVWAI RDGRDAAEGI HAYAKAKAEA PVAVA AE

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Macromolecule #3: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #4: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 4 / Number of copies: 4 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #6: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 6 / Number of copies: 3 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

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

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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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Startup modelType of model: OTHER / Details: NEGATIVE STAIN EM RECONSTRUCTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 47735
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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