1F3J | pdb_00001f3j

HISTOCOMPATIBILITY ANTIGEN I-AG7

PDB DOI: https://doi.org/10.2210/pdb1F3J/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Gallus gallus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2000-06-04 Released: 2000-09-20
Deposition Author(s): Latek, R.R., Unanue, E.R., Fremont, D.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.299 (Depositor)
R-Value Work:
0.221 (Depositor)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Structural basis of peptide binding and presentation by the type I diabetes-associated MHC class II molecule of NOD mice.

Latek, R.R., Suri, A., Petzold, S.J., Nelson, C.A., Kanagawa, O., Unanue, E.R., Fremont, D.H.

(2000) Immunity 12: 699-710

PubMed: 10894169 Search on PubMed
DOI: https://doi.org/10.1016/s1074-7613(00)80220-4
Primary Citation Related Structures:
1F3J

PubMed Abstract:
We have determined the crystal structure of I-Ag7, an integral component in murine type I diabetes development. Several features distinguish I-Ag7 from other non-autoimmune-associated MHC class II molecules, including novel peptide and heterodimer pairing interactions. The binding groove of I-Ag7 is unusual at both terminal ends, with a potentially solvent-exposed channel at the base of the P1 pocket and a widened entrance to the P9 pocket. Peptide binding studies with variants of the hen egg lysozyme I-Ag7 epitope HEL(11-25) support a comprehensive structure-based I-Ag7 binding motif. Residues critical for T cell recognition were investigated with a panel of HEL(11-25)-restricted clones, which uncovered P1 anchor-dependent structural variations. These results establish a framework for future experiments directed at understanding the role of I-Ag7 in autoimmunity.

Organizational Affiliation

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

Macromolecule Content

Total Structure Weight: 90.62 kDa
Atom Count: 6,464
Modeled Residue Count: 766
Deposited Residue Count: 766
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN	A, D	182	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P04228 (Mus musculus) Explore P04228 Go to UniProtKB: P04228
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04228
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain D
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS II NOD	B, E	187	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q31135 (Mus musculus) Explore Q31135 Go to UniProtKB: Q31135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q31135
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain E
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME C	C [auth P], F [auth Q]	14	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth E] SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth B] J [auth D] K [auth D] G [auth A], H [auth A], I [auth B], J [auth D], K [auth D], L [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.299 (Depositor)
R-Value Work: 0.221 (Depositor)
R-Value Observed: 0.221 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.54	α = 90
b = 109.54	β = 90
c = 176.36	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2000-09-20

Deposition Author(s):

Latek, R.R.

Unanue, E.R.

Fremont, D.H.

Revision History (Full details and data files)

Version 1.0: 2000-09-20
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2011-11-16
Changes: Atomic model
Version 1.4: 2017-10-04
Changes: Refinement description
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.6: 2023-08-09
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.7: 2024-10-30
Changes: Structure summary