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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.270 (Depositor), 0.279 (DCC)
R-Value Work:
0.200 (Depositor), 0.208 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

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.

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

Find similar proteins by:

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

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Light Chain	B [auth L]	219	Mus musculus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain E [auth L] SDF format, chain D [auth H] MOL2 format, chain F [auth L] MOL2 format, chain E [auth L] MOL2 format, chain D [auth H] mmCIF format, chain F [auth L] mmCIF format, chain E [auth L] mmCIF format, chain D [auth H]	D [auth H], E [auth L], F [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain E [auth L] Focus chain F [auth L] Interactions & Density Focus chain D [auth H] Focus chain E [auth L] Focus chain F [auth L]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L] mmCIF format, chain G [auth L]	G [auth L]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.270 (Depositor), 0.279 (DCC)
R-Value Work: 0.200 (Depositor), 0.208 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.