8STL

Crystal Structure of Nanobody PIK3_Nb16 against wild-type PI3Kalpha

• PDB DOI: https://doi.org/10.2210/pdb8STL/pdb

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


• Deposited: 2023-05-10 Released: 2024-05-22 
• Deposition Author(s): Nwafor, J.N., Srinivasan, L., Chen, Z., Gabelli, S.B., Iheanacho, A., Alzogaray, V., Klinke, S.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.255 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Development of isoform specific nanobodies for Class I PI3Ks

Nwafor, J.N., Srinivasan, L., Chen, Z., Gabelli, S.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.21 kDa 
• Atom Count: 4,307 
• Modelled Residue Count: 491 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody PIK3_Nb16	A [auth C], B, C [auth A], D	141	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth C], F [auth C], G [auth B], H [auth B], I [auth B], J [auth B], K [auth A], L [auth A], M [auth A], N [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.255 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.607	α = 90
b = 59.383	β = 111.06
c = 70.702	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Nwafor, J.N., Srinivasan, L., Chen, Z., Gabelli, S.B., Iheanacho, A., Alzogaray, V., Klinke, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	--

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release