8SFZ

High Affinity nanobodies against GFP

• PDB DOI: https://doi.org/10.2210/pdb8SFZ/pdb

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


• Deposited: 2023-04-11 Released: 2024-05-22 
• Deposition Author(s): Ketaren, N.E., Rout, M.P., Bonanno, J.B., Almo, S.C.
• 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: 1.90 Å
• R-Value Free: 0.231 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Starting Model: experimental

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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 134.68 kDa 
• Atom Count: 8,752 
• Modelled Residue Count: 1,061 
• Deposited Residue Count: 1,194 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LaG35	A [auth C], B [auth A], C [auth B]	145	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	D, F	253	Aequorea victoria	Mutation(s): 1  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	E	253	Aequorea victoria	Mutation(s): 1  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	I [auth B], J [auth D], K [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	G [auth C], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	D, F	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY
CRO	E	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.231 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.649	α = 90
b = 101.731	β = 90
c = 184.482	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Ketaren, N.E., Rout, M.P., Bonanno, J.B., Almo, S.C.

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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: 2024-05-22
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary