8PIH | pdb_00008pih

Structure of Api m1 in complex with two nanobodies

• PDB DOI: https://doi.org/10.2210/pdb8PIH/pdb

• Classification: ALLERGEN
• Organism(s): Apis mellifera, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-21 Released: 2024-05-08 
• Deposition Author(s): Aagaard, J.B., Gandini, R., Spillner, E., Miehe, M., Andersen, G.R.
• Funding Organization(s): Danish Council for Independent Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Nanobody-based IgG formats as blocking antibodies of the major honeybee venom allergen Api m 1

Aagaard, J.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.69 kDa 
• Atom Count: 3,017 
• Modeled Residue Count: 361 
• Deposited Residue Count: 378 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2	A	133	Apis mellifera	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P00630 (Apis mellifera) Explore P00630  Go to UniProtKB:  P00630

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody AM1-4	B	127	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobdoy AM1-1	C	118	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.96	α = 90
b = 51.33	β = 120.78
c = 73.25	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: 2024-05-08 
Deposition Author(s): Aagaard, J.B., Gandini, R., Spillner, E., Miehe, M., Andersen, G.R.

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

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary