5OJM

Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25

• PDB DOI: https://doi.org/10.2210/pdb5OJM/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): synthetic construct, Homo sapiens, Lama glama
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2017-07-21 Released: 2017-10-04 
• Deposition Author(s): Miller, P.S., Scott, S., Masiulis, S., De Colibus, L., Pardon, E., Steyaert, J., Aricescu, A.R.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council, Medical Research Council (United Kingdom), Wellcome Trust, Human Frontier Science Program

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.234 
• R-Value Observed: 0.234 

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A5B5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: scanning transmission electron microscopy

Macromolecule Content

• Total Structure Weight: 296.52 kDa 
• Atom Count: 18,538 
• Modelled Residue Count: 2,270 
• Deposited Residue Count: 2,600 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5	A, B, C, D, E	395	synthetic construct, Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P31644 (Homo sapiens) Explore P31644  Go to UniProtKB:  P31644
PHAROS:  P31644 GTEx:  ENSG00000186297
Find proteins for P28472 (Homo sapiens) Explore P28472  Go to UniProtKB:  P28472
PHAROS:  P28472 GTEx:  ENSG00000166206
UniProt Groups	P31644P28472

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody Nb25	F [auth K], G [auth L], H [auth M], I [auth N], J [auth O]	125	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth F], L [auth G], M [auth H]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N [auth I], O [auth J]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth A], Q [auth B], R [auth C], S [auth D], T [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.234 
• R-Value Observed: 0.234 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.35	α = 90
b = 139.94	β = 102.25
c = 191.5	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-04 
Deposition Author(s): Miller, P.S., Scott, S., Masiulis, S., De Colibus, L., Pardon, E., Steyaert, J., Aricescu, A.R.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M024709/1
Medical Research Council (United Kingdom)	United Kingdom	MR/L009609/1
Medical Research Council (United Kingdom)	United Kingdom	MC_UP_1201/15
Wellcome Trust	United Kingdom	105247/Z/14/Z
Human Frontier Science Program	France	RGP0065/2014
Wellcome Trust	United Kingdom	090532/Z/09/Z

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary