8R61 | pdb_00008r61

Structure of IgE delta epsilon 3-4 in complex with a kappa binding nanobody

• PDB DOI: https://doi.org/10.2210/pdb8R61/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-20 Released: 2023-11-29 
• Deposition Author(s): Andersen, G.R., Gandini, R.
• Funding Organization(s): Danish Council for Independent Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.275 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.232 (Depositor) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

The dynamics of hinge flexibility in receptor bound immunoglobulin E revealed by electron microscopy

Jensen, R.K., Miehe, M., Gandini, R., Jorgensen, M.H., Spillner, E., Andersen, G.R.

(2023) bioRxiv 

• DOI: https://doi.org/10.1101/2023.02.17.528943

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 442.67 kDa 
• Atom Count: 25,344 
• Modeled Residue Count: 3,360 
• Deposited Residue Count: 4,098 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin E VH-Ceps1-Ceps1	A, D, G, J, M, P	346	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HMM5 IgE light chain	B, E, H, K, N, Q	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
kappa binding nanobody	C, F, I, L, O, R	120	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.275 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.232 (Depositor) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.1	α = 90
b = 132.49	β = 118.843
c = 154.53	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Andersen, G.R., Gandini, R.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	0135-00061B

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2024-06-12
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary