7W85

Structural of the filamentous Escherichia coli glutamine synthetase

PDB DOI: https://doi.org/10.2210/pdb7W85/pdb
EM Map EMD-32352: EMDB EMDataResource

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Escherichia coli BL21(DE3)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-12-07 Released: 2022-04-06
Deposition Author(s): Huang, P.-C., Chen, S.-K., Wu, K.-P.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan), Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.94 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

Structural basis for the helical filament formation of Escherichia coli glutamine synthetase.

Huang, P.C., Chen, S.K., Chiang, W.H., Ho, M.R., Wu, K.P.

(2022) Protein Sci 31: e4304-e4304

PubMed: 35481643 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.4304
Primary Citation of Related Structures:
7W85

PubMed Abstract:
Escherichia coli glutamine synthetase (EcGS) spontaneously forms a dodecamer that catalytically converts glutamate to glutamine. EcGS stacks with other dodecamers to create a filament-like polymer visible under transmission electron microscopy. Filamentous EcGS is induced by environmental metal ions. We used cryo-electron microscopy (cryo-EM) to decipher the structure of metal ion (nickel)-induced EcGS helical filament at a sub-3Å resolution. EcGS filament formation involves stacking of native dodecamers by chelating nickel ions to residues His5 and His13 in the first N-terminal helix (H1). His5 and His13 from paired parallel H1 helices provide salt bridges and hydrogen bonds to tightly stack two dodecamers. One subunit of the EcGS filament hosts two nickel ions, whereas the dodecameric interface and the ATP/Mg-binding site both host a nickel ion each. We reveal that upon adding glutamate or ATP for catalytic reactions, nickel-induced EcGS filament reverts to individual dodecamers. Such tunable filament formation is often associated with stress responses. Our results provide detailed structural information on the mechanism underlying reversible and tunable EcGS filament formation.

Organizational Affiliation

Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Macromolecule Content

Total Structure Weight: 1,249.66 kDa
Atom Count: 81,522
Modelled Residue Count: 10,440
Deposited Residue Count: 11,256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine synthetase	A B C D E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y]	469	Escherichia coli BL21(DE3)	Mutation(s): 0 Gene Names: glnA, b3870, JW3841 EC: 6.3.1.2
UniProt
Find proteins for P0A9C5 (Escherichia coli (strain K12)) Explore P0A9C5 Go to UniProtKB: P0A9C5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A9C5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth Q] SDF format, chain BA [auth B] SDF format, chain BB [auth R] SDF format, chain CA [auth C] SDF format, chain CB [auth S] SDF format, chain DA [auth C] SDF format, chain DB [auth S] SDF format, chain EA [auth D] SDF format, chain EB [auth U] SDF format, chain FA [auth D] SDF format, chain FB [auth U] SDF format, chain GA [auth E] SDF format, chain GB [auth V] SDF format, chain HA [auth E] SDF format, chain HB [auth V] SDF format, chain IA [auth F] SDF format, chain IB [auth W] SDF format, chain JA [auth F] SDF format, chain JB [auth W] SDF format, chain KA [auth G] SDF format, chain KB [auth X] SDF format, chain LA [auth G] SDF format, chain LB [auth X] SDF format, chain MA [auth H] SDF format, chain MB [auth Y] SDF format, chain NA [auth H] SDF format, chain NB [auth Y] SDF format, chain OA [auth I] SDF format, chain PA [auth I] SDF format, chain QA [auth J] SDF format, chain RA [auth J] SDF format, chain SA [auth K] SDF format, chain TA [auth K] SDF format, chain UA [auth L] SDF format, chain VA [auth L] SDF format, chain WA [auth M] SDF format, chain XA [auth N] SDF format, chain Y [auth A] SDF format, chain YA [auth O] SDF format, chain Z [auth A] SDF format, chain ZA [auth P] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth Q] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth R] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth S] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth S] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth U] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth U] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth V] MOL2 format, chain HA [auth E] MOL2 format, chain HB [auth V] MOL2 format, chain IA [auth F] MOL2 format, chain IB [auth W] MOL2 format, chain JA [auth F] MOL2 format, chain JB [auth W] MOL2 format, chain KA [auth G] MOL2 format, chain KB [auth X] MOL2 format, chain LA [auth G] MOL2 format, chain LB [auth X] MOL2 format, chain MA [auth H] MOL2 format, chain MB [auth Y] MOL2 format, chain NA [auth H] MOL2 format, chain NB [auth Y] MOL2 format, chain OA [auth I] MOL2 format, chain PA [auth I] MOL2 format, chain QA [auth J] MOL2 format, chain RA [auth J] MOL2 format, chain SA [auth K] MOL2 format, chain TA [auth K] MOL2 format, chain UA [auth L] MOL2 format, chain VA [auth L] MOL2 format, chain WA [auth M] MOL2 format, chain XA [auth N] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth O] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth P]	AA [auth B] AB [auth Q] BA [auth B] BB [auth R] CA [auth C] AA [auth B], AB [auth Q], BA [auth B], BB [auth R], CA [auth C], CB [auth S], DA [auth C], DB [auth S], EA [auth D], EB [auth U], FA [auth D], FB [auth U], GA [auth E], GB [auth V], HA [auth E], HB [auth V], IA [auth F], IB [auth W], JA [auth F], JB [auth W], KA [auth G], KB [auth X], LA [auth G], LB [auth X], MA [auth H], MB [auth Y], NA [auth H], NB [auth Y], OA [auth I], PA [auth I], QA [auth J], RA [auth J], SA [auth K], TA [auth K], UA [auth L], VA [auth L], WA [auth M], XA [auth N], Y [auth A], YA [auth O], Z [auth A], ZA [auth P]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth Q] Focus chain BA [auth B] Focus chain BB [auth R] Focus chain CA [auth C] Focus chain CB [auth S] Focus chain DA [auth C] Focus chain DB [auth S] Focus chain EA [auth D] Focus chain EB [auth U] Focus chain FA [auth D] Focus chain FB [auth U] Focus chain GA [auth E] Focus chain GB [auth V] Focus chain HA [auth E] Focus chain HB [auth V] Focus chain IA [auth F] Focus chain IB [auth W] Focus chain JA [auth F] Focus chain JB [auth W] Focus chain KA [auth G] Focus chain KB [auth X] Focus chain LA [auth G] Focus chain LB [auth X] Focus chain MA [auth H] Focus chain MB [auth Y] Focus chain NA [auth H] Focus chain NB [auth Y] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain WA [auth M] Focus chain XA [auth N] Focus chain Y [auth A] Focus chain YA [auth O] Focus chain Z [auth A] Focus chain ZA [auth P] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth Q] Focus chain BA [auth B] Focus chain BB [auth R] Focus chain CA [auth C] Focus chain CB [auth S] Focus chain DA [auth C] Focus chain DB [auth S] Focus chain EA [auth D] Focus chain EB [auth U] Focus chain FA [auth D] Focus chain FB [auth U] Focus chain GA [auth E] Focus chain GB [auth V] Focus chain HA [auth E] Focus chain HB [auth V] Focus chain IA [auth F] Focus chain IB [auth W] Focus chain JA [auth F] Focus chain JB [auth W] Focus chain KA [auth G] Focus chain KB [auth X] Focus chain LA [auth G] Focus chain LB [auth X] Focus chain MA [auth H] Focus chain MB [auth Y] Focus chain NA [auth H] Focus chain NB [auth Y] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain WA [auth M] Focus chain XA [auth N] Focus chain Y [auth A] Focus chain YA [auth O] Focus chain Z [auth A] Focus chain ZA [auth P]