8FIF | pdb_00008fif

A2.3 Nanobody In Complex With Microcystin-LR

• PDB DOI: https://doi.org/10.2210/pdb8FIF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Lama glama, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-12-16 Released: 2023-12-20 
• Deposition Author(s): Arenas, R., Tabares-da Rosa, S., Gonzalez-Sapienza, G., Wilson, D.K.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

A2.3 Nanobody In Complex With Microcystin-LR

Arenas, R., Tabares-da Rosa, S., Gonzalez-Sapienza, G., Wilson, D.K.

To be published.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.1 kDa 
• Atom Count: 3,123 
• Modeled Residue Count: 379 
• Deposited Residue Count: 408 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single Domain Camelid Nanobody VHH A2.3	A, B, C	129	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Microcystin-LR	D, E [auth F], F [auth G]	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MAA	D, E [auth F], F [auth G]	L-PEPTIDE LINKING	C4 H9 N O2		ALA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001031	D, E [auth F], F [auth G]	Microcystin-LR (MCLR) bound form	Oligopeptide / Toxin

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.240 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.097	α = 90
b = 101.317	β = 90
c = 102.412	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Arenas, R., Tabares-da Rosa, S., Gonzalez-Sapienza, G., Wilson, D.K.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary