1i3r

CRYSTAL STRUCTURE OF A MUTANT IEK CLASS II MHC MOLECULE

Method: X-RAY DIFFRACTION

1. Protein Identity and Related Structures Protein Identity & Related Structures

H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN

Mus musculus

UniProt P04224

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 8 其他Polymer 4 FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN × 4 (P02089) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 water × 8 Consistent with protein count
2 Other combination Heteromer Protein 2 其他Polymer 1 FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN × 1 (P02089) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2 Consistent with protein count
3 Other combination Heteromer Protein 2 其他Polymer 1 FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN × 1 (P02089) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2 Consistent with protein count
4 Other combination Heteromer Protein 2 其他Polymer 1 FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN × 1 (P02089) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2 Consistent with protein count
5 Other combination Heteromer Protein 2 其他Polymer 1 FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN × 1 (P02089) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2 Consistent with protein count
6 Other combination Heteromer Protein 4 其他Polymer 2 FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN × 2 (P02089) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 water × 4 Consistent with protein count
7 Other combination Heteromer Protein 4 其他Polymer 2 FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN × 2 (P02089) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name HA22_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–192; UniProt 26–217 Author chain C; PDBConstruct 1–192; UniProt 26–217 Author chain E; PDBConstruct 1–192; UniProt 26–217 Author chain G; PDBConstruct 1–192; UniProt 26–217

FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN

Mus musculus

UniProt P02089

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 8 其他Polymer 4 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN × 4 (P04224) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 water × 8 Consistent with protein count
2 Other combination Heteromer Protein 2 其他Polymer 1 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN × 1 (P04224) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2 Consistent with protein count
3 Other combination Heteromer Protein 2 其他Polymer 1 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN × 1 (P04224) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2 Consistent with protein count
4 Other combination Heteromer Protein 2 其他Polymer 1 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN × 1 (P04224) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2 Consistent with protein count
5 Other combination Heteromer Protein 2 其他Polymer 1 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN × 1 (P04224) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2 Consistent with protein count
6 Other combination Heteromer Protein 4 其他Polymer 2 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN × 2 (P04224) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 water × 4 Consistent with protein count
7 Other combination Heteromer Protein 4 其他Polymer 2 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN × 2 (P04224) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name HBB2_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 5–17; UniProt 64–76 Author chain D; PDBConstruct 5–17; UniProt 64–76 Author chain F; PDBConstruct 5–17; UniProt 64–76 Author chain H; PDBConstruct 5–17; UniProt 64–76

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

2. Structure Basics 2. Structure Basics

Entry ID entry_id1i3r
Deposition date deposition_date2001-02-15
Structure title titleCRYSTAL STRUCTURE OF A MUTANT IEK CLASS II MHC MOLECULE
Keywords keywordsMHC ClassII, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1i3r__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1i3r__assembly_4__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1i3r__assembly_4__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)24.82 Å
Rg (electron density)23.78 Å
Total Rg24.68 Å
Atom count3248
Residues398
Excluded volume57286 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1i3r__assembly_1__model_1 octameric (8) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1i3r__assembly_2__model_1 dimeric (2) Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1i3r__assembly_3__model_1 dimeric (2) Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1i3r__assembly_4__model_1 dimeric (2) Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1i3r__assembly_5__model_1 dimeric (2) Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 1i3r__assembly_6__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 1i3r__assembly_7__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download

4. Crystallography and Experiment 4. Crystallography & Experiment

5. Entities and Polymers Entities & Polymers (5)

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd1i3ra1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1i3ra2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1i3rb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1i3rb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1i3rc1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1i3rc2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1i3rd1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1i3rd2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1i3re1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1i3re2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1i3rf1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1i3rf2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1i3rg1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1i3rg2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1i3rh1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1i3rh2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain

CATH v4.4 (16 domains)

Domain ID domain_id1i3rA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1i3rA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1i3rB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1i3rB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1i3rC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1i3rC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1i3rD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1i3rD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1i3rE01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1i3rE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1i3rF01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1i3rF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1i3rG01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1i3rG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1i3rH01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1i3rH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

7. Citations (1)