7FGL | pdb_00007fgl

The complex structure of PHF core domain peptide of tau, VQIVYK, and antibody's Fab domain.

• PDB DOI: https://doi.org/10.2210/pdb7FGL/pdb

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


• Deposited: 2021-07-27 Released: 2022-07-27 
• Deposition Author(s): Tsuchida, 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: 2.10 Å
• R-Value Free: 
  0.270 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

The cross-reaction complex structure with VQIVYK of tau and the antibody's Fab domain.

Tomohiro, T., Takahiro, T., Katsushiro, M., Yasuko, I., Katsuhiko, M., Taizo, T., Toshimitsu, I., Koji, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.91 kDa 
• Atom Count: 3,785 
• Modeled Residue Count: 444 
• Deposited Residue Count: 444 
• Unique protein chains: 3

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]	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VQIVYK	C	6	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth H], E [auth L], F [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NH4	G [auth L]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.270 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.98	α = 90
b = 70.72	β = 90
c = 118.03	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
BALBES	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., 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: 2024-11-13
  Changes: Structure summary