[English] 日本語
![](img/lk-miru.gif)
- EMDB-10104: Structure of Azospirillum brasilense Glutamate Synthase in a4b4 o... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-10104 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Azospirillum brasilense Glutamate Synthase in a4b4 oligomeric state. | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
Function / homology | ![]() glutamate synthase (NADPH) / glutamate synthase (NADPH) activity / glutamate synthase (NADH) activity / L-glutamate biosynthetic process / ammonia assimilation cycle / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Swuec P | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 104.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.9 KB | Display | ![]() |
Images | ![]() | 167.6 KB | ||
Masks | ![]() | 111.5 MB | ![]() | |
Others | ![]() ![]() ![]() | 87.5 MB 87.7 MB 87.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s6sMC ![]() 6s6tC ![]() 6s6uC ![]() 6s6xC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.426 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: #1
File | emd_10104_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_10104_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_10104_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Glutamate Synthase complex in a4b4 oligomeric state
Entire | Name: Glutamate Synthase complex in a4b4 oligomeric state |
---|---|
Components |
|
-Supramolecule #1: Glutamate Synthase complex in a4b4 oligomeric state
Supramolecule | Name: Glutamate Synthase complex in a4b4 oligomeric state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Glutamate synthase [NADPH] large chain
Macromolecule | Name: 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: ![]() |
Molecular weight | Theoretical: 166.224734 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Glutamate synthase [NADPH] small chain
Macromolecule | Name: Glutamate synthase [NADPH] small chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: glutamate synthase (NADPH) |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 52.425109 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: FLAVIN MONONUCLEOTIDE
Macromolecule | Name: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: FMN |
---|---|
Molecular weight | Theoretical: 456.344 Da |
Chemical component information | ![]() ChemComp-FMN: |
-Macromolecule #4: FE3-S4 CLUSTER
Macromolecule | Name: FE3-S4 CLUSTER / type: ligand / ID: 4 / Number of copies: 4 / Formula: F3S |
---|---|
Molecular weight | Theoretical: 295.795 Da |
Chemical component information | ![]() ChemComp-F3S: |
-Macromolecule #5: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 8 / Formula: SF4 |
---|---|
Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ![]() ChemComp-FS1: |
-Macromolecule #6: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 6 / Number of copies: 4 / Formula: FAD |
---|---|
Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ![]() ChemComp-FAD: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 3 mg/mL |
---|---|
Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |