8G0I

High Affinity nanobodies against GFP

• PDB DOI: https://doi.org/10.2210/pdb8G0I/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Aequorea victoria, Lama glama
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-01-31 Released: 2024-03-20 
• Deposition Author(s): Ketaren, N.E., Rout, M.P., Almo, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.181 
• R-Value Observed: 0.187 

Literature

High Affinity nanobodies against GFP

Ketaren, N.E., Rout, M.P., Almo, 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: 43.69 kDa 
• Atom Count: 2,721 
• Modelled Residue Count: 339 
• Deposited Residue Count: 390 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	253	Aequorea victoria	Mutation(s): 1  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LaG24 Nanobody	B [auth D]	137	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth D], F [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.181 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.1	α = 90
b = 86.666	β = 90
c = 52.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Ketaren, N.E., Rout, M.P., Almo, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release