6S6U

Structure of Azospirillum brasilense Glutamate Synthase in a6b4 oligomeric state.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM Structures of Azospirillum brasilense Glutamate Synthase in Its Oligomeric Assemblies.

Swuec, P.Chaves-Sanjuan, A.Camilloni, C.Vanoni, M.A.Bolognesi, M.

(2019) J Mol Biol 431: 4523-4526

  • DOI: 10.1016/j.jmb.2019.08.011
  • Primary Citation of Related Structures:  
    6S6S, 6S6T, 6S6U, 6S6X

  • PubMed 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 unit hosts an α-subunit (αGltS) and a β-subunit (βGltS) that assemble in different αβ oligomers in solution ...

    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 (α 4 β 3 , α 4 β 4 , α 6 β 4 and α 6 β 6 , 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] +1,+2 clusters within βGltS.


    Organizational Affiliation

    Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy. Electronic address: martino.bolognesi@unimi.it.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate synthase [NADPH] large chain
A, B, C, D, E, F
A, B, C, D, E, F
1,515Azospirillum brasilenseMutation(s): 0 
Gene Names: gltB
EC: 1.4.1.13
UniProt
Find proteins for Q05755 (Azospirillum brasilense)
Explore Q05755 
Go to UniProtKB:  Q05755
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05755
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate synthase [NADPH] small chainG, H, I, J482Azospirillum brasilenseMutation(s): 0 
Gene Names: gltD
EC: 1.4.1.13
UniProt
Find proteins for Q05756 (Azospirillum brasilense)
Explore Q05756 
Go to UniProtKB:  Q05756
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05756
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
BA [auth H],
EA [auth I],
HA [auth J],
Y [auth G]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
U [auth F]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth H],
CA [auth I],
DA [auth I],
FA [auth J],
GA [auth J],
AA [auth H],
CA [auth I],
DA [auth I],
FA [auth J],
GA [auth J],
W [auth G],
X [auth G],
Z [auth H]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E],
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E],
V [auth F]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Database references