6H7N | pdb_00006h7n

ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST XAMOTEROL AND NANOBODY Nb6B9

• PDB DOI: https://doi.org/10.2210/pdb6H7N/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli K-12, Meleagris gallopavo, Lama glama
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2018-07-31 Released: 2018-10-17 
• Deposition Author(s): Warne, T., Edwards, P.C., Dore, A.S., Leslie, A.G.W., Tate, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.266 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Models: experimental

Literature

Molecular basis for high affinity agonist binding in GPCRs

Warne, T., Edwards, P.C., Dore, A.S., Leslie, A.G.W., Tate, C.G.

(2018) bioRxiv 

• DOI: https://doi.org/10.1101/436212

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 122.27 kDa 
• Atom Count: 8,211 
• Modeled Residue Count: 1,031 
• Deposited Residue Count: 1,074 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin 1	A [auth E], C [auth F]	109	Escherichia coli K-12	Mutation(s): 2  Gene Names: trxA, fipA, tsnC, b3781, JW5856
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25  Go to UniProtKB:  P0AA25

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-1 adrenergic receptor	B [auth A], D [auth B]	307	Meleagris gallopavo	Mutation(s): 6  Gene Names: ADRB1 Membrane Entity: Yes
UniProt
Find proteins for P07700 (Meleagris gallopavo) Explore P07700  Go to UniProtKB:  P07700

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Camelid antibody fragment Nb6B9	E [auth C], F [auth D]	121	Lama glama	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2CV	I [auth A], J [auth A], K [auth A], L [auth B], O [auth B]	HEGA-10 C18 H37 N O7 ITEIKACYSCODFV-ATLSCFEFSA-N
FVK	G [auth A], M [auth B]	~{N}-[2-[[(2~{S})-2-oxidanyl-3-(4-oxidanylphenoxy)propyl]amino]ethyl]morpholine-4-carboxamide C16 H25 N3 O5 DXPOSRCHIDYWHW-AWEZNQCLSA-N
NA	H [auth A], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.266 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.41	α = 90
b = 121.533	β = 90
c = 130.247	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Warne, T., Edwards, P.C., Dore, A.S., Leslie, A.G.W., Tate, C.G.

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary