8RAL

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)

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
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14434
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14483
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CL3E peptide	C	13	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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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	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G75436UI GlyCosmos: G75436UI GlyGen: G75436UI

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
VHF Query on 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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-06

Deposition Author(s):

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 (Full details and data files)

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