2icw

Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HLA class II histocompatibility antigen, DR alpha chain

Homo sapiens

UniProt P01903

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) haemagglutinin peptide × 1 Mycoplasma arthritidis mitogen × 1 (Q48898) T-cell receptor alpha chain V × 1 (P01738) T-cell receptor beta chain V × 1 (P04213) water × 6 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) haemagglutinin peptide × 1 Mycoplasma arthritidis mitogen × 1 (Q48898) T-cell receptor alpha chain V × 1 (P01738) T-cell receptor beta chain V × 1 (P04213) water × 6 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name 2DRA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–179; UniProt 28–206 Author chain D; PDBConstruct 1–179; UniProt 28–206

HLA class II histocompatibility antigen, DRB1-1 beta chain

Homo sapiens

UniProt P04229

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) haemagglutinin peptide × 1 Mycoplasma arthritidis mitogen × 1 (Q48898) T-cell receptor alpha chain V × 1 (P01738) T-cell receptor beta chain V × 1 (P04213) water × 6 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) haemagglutinin peptide × 1 Mycoplasma arthritidis mitogen × 1 (Q48898) T-cell receptor alpha chain V × 1 (P01738) T-cell receptor beta chain V × 1 (P04213) water × 6 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name 2B11_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–190; UniProt 30–219 Author chain E; PDBConstruct 1–190; UniProt 30–219

Mycoplasma arthritidis mitogen

Mycoplasma arthritidis

UniProt Q48898

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) haemagglutinin peptide × 1 T-cell receptor alpha chain V × 1 (P01738) T-cell receptor beta chain V × 1 (P04213) water × 6 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) haemagglutinin peptide × 1 T-cell receptor alpha chain V × 1 (P01738) T-cell receptor beta chain V × 1 (P04213) water × 6 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name Q48898_MYCAT
Isoform —
PDB entities 4
Chains and sequence ranges Author chain G; PDBConstruct 1–213; UniProt 26–238 Author chain H; PDBConstruct 1–213; UniProt 26–238

T-cell receptor alpha chain V

Mus musculus

UniProt P01738

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) haemagglutinin peptide × 1 Mycoplasma arthritidis mitogen × 1 (Q48898) T-cell receptor beta chain V × 1 (P04213) water × 6 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) haemagglutinin peptide × 1 Mycoplasma arthritidis mitogen × 1 (Q48898) T-cell receptor beta chain V × 1 (P04213) water × 6 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name TVA1_MOUSE
Isoform —
PDB entities 5
Chains and sequence ranges Author chain I; PDBConstruct 1–110; UniProt 21–130 Author chain K; PDBConstruct 1–110; UniProt 21–130

T-cell receptor beta chain V

Mus musculus

UniProt P04213

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) haemagglutinin peptide × 1 Mycoplasma arthritidis mitogen × 1 (Q48898) T-cell receptor alpha chain V × 1 (P01738) water × 6 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) haemagglutinin peptide × 1 Mycoplasma arthritidis mitogen × 1 (Q48898) T-cell receptor alpha chain V × 1 (P01738) water × 6 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name TVB5_MOUSE
Isoform —
PDB entities 6
Chains and sequence ranges Author chain J; PDBConstruct 1–80; UniProt 9–88 Author chain L; PDBConstruct 1–80; UniProt 9–88

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id2icw
Deposition date deposition_date2006-09-13
Structure title titleCrystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule
Keywords keywordsTCR, MHC, superantigen, protein-protein complex, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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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.

2icw__assembly_1__model_1

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

Download this curve (.dat)

2icw__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2icw__assembly_1__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)34.12 Å
Rg (electron density)34.02 Å
Total Rg34.40 Å
Atom count6583
Residues809
Excluded volume116980 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2icw__assembly_1__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2icw__assembly_2__model_1 hexameric (6) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (14 domains)

Domain ID domain_idd2icwa1
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_idd2icwa2
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_idd2icwb1
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_idd2icwb2
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_idd2icwd1
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_idd2icwd2
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_idd2icwe1
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_idd2icwe2
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_idd2icwg_
Class classa — All alpha proteins
Fold Fold folda.202 — Superantigen MAM
Superfamily Superfamily superfamilya.202.1 — Superantigen MAM
Family Family familya.202.1.1 — Superantigen MAM
Domain ID domain_idd2icwh_
Class classa — All alpha proteins
Fold Fold folda.202 — Superantigen MAM
Superfamily Superfamily superfamilya.202.1 — Superantigen MAM
Family Family familya.202.1.1 — Superantigen MAM
Domain ID domain_idd2icwj1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2icwj2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2icwl2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2icwl3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (16 domains)

Domain ID domain_id2icwA01
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_id2icwA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2icwB01
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_id2icwB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2icwD01
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_id2icwD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2icwE01
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_id2icwE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2icwG01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily390 — Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1
Domain ID domain_id2icwG02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily530 — mam-mhc complex, Chain D, Domain 2
Domain ID domain_id2icwH01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily390 — Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1
Domain ID domain_id2icwH02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily530 — mam-mhc complex, Chain D, Domain 2
Domain ID domain_id2icwI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2icwJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2icwK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2icwL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)