8APY

Crystal structure of the H12A variant of the KDEL receptor bound to sybody

• PDB DOI: https://doi.org/10.2210/pdb8APY/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Gallus gallus, synthetic construct
• Expression System: Saccharomyces cerevisiae, Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2022-08-10 Released: 2023-08-23 
• Deposition Author(s): Parker, J.L., Smith, K., Newstead, S.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.329 
• R-Value Work: 0.268 
• R-Value Observed: 0.271 

Literature

Crystal structure of the H12A variant of the KDEL receptor bound to sybody

Parker, J.L., Smith, K., Newstead, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.38 kDa 
• Atom Count: 2,681 
• Modelled Residue Count: 325 
• Deposited Residue Count: 333 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ER lumen protein-retaining receptor 2	A	212	Gallus gallus	Mutation(s): 1  Gene Names: KDELR2, RCJMB04_8l23 Membrane Entity: Yes
UniProt
Find proteins for Q5ZKX9 (Gallus gallus) Explore Q5ZKX9  Go to UniProtKB:  Q5ZKX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic nanobody	B [auth C]	121	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	C [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.329 
• R-Value Work: 0.268 
• R-Value Observed: 0.271 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.19	α = 90
b = 71.09	β = 90
c = 133.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Parker, J.L., Smith, K., Newstead, S.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	219531/Z/19/Z

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release