7FGK | pdb_00007fgk

The Fab antibody single structure against tau protein.

• PDB DOI: https://doi.org/10.2210/pdb7FGK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2021-07-27 Released: 2022-07-27 
• Deposition Author(s): Tsuchida, T., Susa, K., Kibiki, T., Tsuchiya, T., Miyamoto, K., In, Y., Minoura, K., Taniguchi, T., Ishida, T., Tomoo, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.299 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Models: experimental

Literature

The free structure of the Fab domain of antibody that recognizes the PHF core region VQIINK in Tau protein.

Tsuchida, T., Susa, K., Kibiki, T., Tsuchiya, T., Miyamoto, K., In, Y., Minoura, K., Taniguchi, T., Ishida, T., Tomoo, K.

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: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 47.2 kDa 
• Atom Count: 3,638 
• Modelled Residue Count: 431 
• Deposited Residue Count: 437 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Heavy Chain	A [auth H]	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Light Chain	B [auth L]	218	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth H], F [auth L]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	D [auth H], E [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.299 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.14	α = 90
b = 70.78	β = 93.55
c = 41.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Tsuchida, T., Susa, K., Kibiki, T., Tsuchiya, T., Miyamoto, K., In, Y., Minoura, K., Taniguchi, T., Ishida, T., Tomoo, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary