8FE1

Alpha1/BetaB Heteromeric Glycine Receptor in 1 mM Glycine 20 uM Ivermectin State


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-throughput reprogramming of an NRPS condensation domain.

Folger, I.B.Frota, N.F.Pistofidis, A.Niquille, D.L.Hansen, D.A.Schmeing, T.M.Hilvert, D.

(2024) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-023-01532-x
  • Primary Citation of Related Structures:  
    8F7F, 8F7G, 8F7H, 8F7I, 8FE1

  • PubMed Abstract: 

    Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogs. Although yeast display is a proven, powerful tool for altering the substrate specificity of gatekeeper adenylation domains in nonribosomal peptide synthetases (NRPSs), comparable strategies for other components of these megaenzymes have not been described. Here we report a high-throughput approach for engineering condensation (C) domains responsible for peptide elongation. We show that a 120-kDa NRPS module, displayed in functional form on yeast, can productively interact with an upstream module, provided in solution, to produce amide products tethered to the yeast surface. Using this system to screen a large C-domain library, we reprogrammed a surfactin synthetase module to accept a fatty acid donor, increasing catalytic efficiency for this noncanonical substrate >40-fold. Because C domains can function as selectivity filters in NRPSs, this methodology should facilitate the precision engineering of these molecular assembly lines.


  • Organizational Affiliation

    Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland. hilvert@ethz.ch.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine receptor subunit alphaZ1A,
B [auth D],
C,
D [auth B]
458Danio rerioMutation(s): 0 
Gene Names: glra1
Membrane Entity: Yes 
UniProt
Find proteins for O93430 (Danio rerio)
Explore O93430 
Go to UniProtKB:  O93430
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93430
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine receptor beta subunit 2591Danio rerioMutation(s): 0 
Gene Names: glrb2zgc:101041glrbbSO:0001217
Membrane Entity: Yes 
UniProt
Find proteins for Q6DC22 (Danio rerio)
Explore Q6DC22 
Go to UniProtKB:  Q6DC22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DC22
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IVM (Subject of Investigation/LOI)
Query on IVM

Download Ideal Coordinates CCD File 
FA [auth C],
H [auth A],
I [auth A],
QA [auth B],
R [auth D]
(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside
C48 H74 O14
AZSNMRSAGSSBNP-XPNPUAGNSA-N
PX4
Query on PX4

Download Ideal Coordinates CCD File 
CA [auth C]
HA [auth C]
J [auth A]
OA [auth B]
RA [auth B]
CA [auth C],
HA [auth C],
J [auth A],
OA [auth B],
RA [auth B],
S [auth D],
U [auth D],
ZA [auth E]
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
PLM
Query on PLM

Download Ideal Coordinates CCD File 
AA [auth D]
BB [auth E]
CB [auth E]
DB [auth E]
EB [auth E]
AA [auth D],
BB [auth E],
CB [auth E],
DB [auth E],
EB [auth E],
FB [auth E],
IA [auth C],
JA [auth C],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
P [auth A],
SA [auth B],
T [auth D],
TA [auth B],
UA [auth B],
VA [auth B],
W [auth D],
WA [auth B],
X [auth D],
XA [auth B],
Y [auth D],
Z [auth D]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth E]
EA [auth C]
G [auth A]
PA [auth B]
Q [auth D]
AB [auth E],
EA [auth C],
G [auth A],
PA [auth B],
Q [auth D],
YA [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
D10
Query on D10

Download Ideal Coordinates CCD File 
GA [auth C]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
GLY (Subject of Investigation/LOI)
Query on GLY

Download Ideal Coordinates CCD File 
BA [auth C],
DA [auth C],
F [auth A],
K [auth A],
V [auth D]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1F32GM142233
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM134896
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM134896-2S1

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references