6S6S | pdb_00006s6s

Structure of Azospirillum brasilense Glutamate Synthase in a4b4 oligomeric state.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6S6S

This is version 1.6 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 Biology 431: 4523-4526

  • DOI: https://doi.org/10.1016/j.jmb.2019.08.011
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 883.56 kDa 
  • Atom Count: 60,044 
  • Modeled Residue Count: 7,752 
  • Deposited Residue Count: 7,988 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate synthase [NADPH] large chain
A, B, C, D
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
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate synthase [NADPH] small chainE [auth G],
F [auth E],
G [auth F],
H		482Azospirillum 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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD


Download:Ideal Coordinates CCD File
BA [auth H],
S [auth G],
V [auth E],
Y [auth F]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN
(Subject of Investigation/LOI)

Query on FMN


Download:Ideal Coordinates CCD File
I [auth A],
K [auth B],
M [auth C],
O [auth D]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
AA [auth H]
Q [auth G]
R [auth G]
T [auth E]
U [auth E]
AA [auth H],
Q [auth G],
R [auth G],
T [auth E],
U [auth E],
W [auth F],
X [auth F],
Z [auth H]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S

Query on F3S


Download:Ideal Coordinates CCD File
J [auth A],
L [auth B],
N [auth C],
P [auth D]		FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.2: 2019-11-20
    Changes: Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Database references
  • Version 1.4: 2025-04-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2025-07-09
    Changes: Data collection
  • Version 1.6: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations