8RAL | pdb_00008ral

CL3E peptide bound to the I-Ab murine MHC class II receptor

• PDB DOI: https://doi.org/10.2210/pdb8RAL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, synthetic construct
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2023-12-01 Released: 2024-11-06 
• Deposition Author(s): Erausquin, E., Urdiciain, A., Serra, P., Santamaria, P., Lopez-Sagaseta, J.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities, European Foundation for the Study of Diabetes (EFSD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.263 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.224 (DCC) 

Starting Model: experimental

Literature

CL3E peptide bound to the I-Ab murine MHC class II receptor

Lopez-Sagaseta, J., Erausquin, E., Urdiciain, A., Serra, P., Santamaria, P.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.11 kDa 
• Atom Count: 3,013 
• Modeled Residue Count: 366 
• Deposited Residue Count: 432 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A-B alpha chain	A	195	Mus musculus	Mutation(s): 1  Gene Names: H2-Aa
UniProt
Find proteins for P14434 (Mus musculus) Explore P14434  Go to UniProtKB:  P14434
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A beta chain	B	224	Mus musculus	Mutation(s): 0  Gene Names: H2-Ab1, H2-iabeta
UniProt
Find proteins for P14483 (Mus musculus) Explore P14483  Go to UniProtKB:  P14483

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CL3E peptide	C	13	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G75436UI GlyCosmos:  G75436UI GlyGen:  G75436UI

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
VHF	B	L-PEPTIDE LINKING	C5 H10 N O7 P		GLU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.263 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.224 (DCC) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.057	α = 90
b = 76.032	β = 90
c = 133.037	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Erausquin, E., Urdiciain, A., Serra, P., Santamaria, P., Lopez-Sagaseta, J.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	RYC201721683
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2021-125493OB-I00
European Foundation for the Study of Diabetes (EFSD)	European Union	--

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release
  
• Version 2.0: 2024-11-27
  Type: Coordinate replacement
  Reason: Polymer backbone linkage
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary