31VO | pdb_000031vo

Crystal structure of amyloid beta 1-15 fragment bound to HLA-DR1

• PDB DOI: https://doi.org/10.2210/pdb31VO/pdb

• Classification: NEUROPEPTIDE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2026-06-24 Released: 2026-09-16 
• Deposition Author(s): Lopez-Sagaseta, J., Erausquin, E., Dichiara-Rodriguez, M.G., Oyon-Olea, L.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: in silico

Literature

Structural presentation of an amyloid beta fragment by HLA

Lopez-Sagaseta, J.

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: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.57 kDa 
• Atom Count: 6,258 
• Modeled Residue Count: 756 
• Deposited Residue Count: 850 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid-beta protein 40,HLA class II histocompatibility antigen DR beta chain	A [auth B], C [auth D]	227	Homo sapiens	Mutation(s): 0  Gene Names: APP, A4, AD1, HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067 GTEx:  ENSG00000142192
Find proteins for D7RIG0 (Homo sapiens) Explore D7RIG0  Go to UniProtKB:  D7RIG0
UniProt Groups	P05067D7RIG0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	B [auth A], D [auth C]	198	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01903-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	E [auth A], F [auth A], H [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.308	α = 90
b = 118.508	β = 109.148
c = 67.126	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Lopez-Sagaseta, J., Erausquin, E., Dichiara-Rodriguez, M.G., Oyon-Olea, L.

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Funding Organization	Location	Grant Number
Other government	Spain	PC24-MEMORIAL-017-003-015

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release