8H8Q

Fab-amyloid beta fragment complex at neutral pH

• PDB DOI: https://doi.org/10.2210/pdb8H8Q/pdb

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


• Deposited: 2022-10-24 Released: 2023-10-25 
• Deposition Author(s): Kita, A., Irie, K., Irie, Y., Matsushima, Y., Miki, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.212 

Literature

Fab-amyloid beta fragment complex at neutral pH

Irie, K., Irie, Y., Matsushima, Y., Kita, A., Miki, K.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 49.54 kDa 
• Atom Count: 3,460 
• Modelled Residue Count: 447 
• Deposited Residue Count: 453 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab	A [auth L]	218	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab	B [auth H]	220	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GLN-LYS-CYS-VAL-PHE-PHE-ALA-GLU-ASP-VAL-GLY-SER-ASN-CYS-GLY	C [auth A]	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067 GTEx:  ENSG00000142192

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	D [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.04	α = 90
b = 94.15	β = 90
c = 115.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Kita, A., Irie, K., Irie, Y., Matsushima, Y., Miki, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release
  
• Version 2.0: 2023-11-29
  Type: Coordinate replacement
  Reason: Atoms with unrealistic or zero occupancies
  Changes: Atomic model, Author supporting evidence, Derived calculations, Refinement description, Structure summary