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_id	2icw
Deposition date deposition_date	2006-09-13
Structure title title	Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule
Keywords keywords	TCR, MHC, superantigen, protein-protein complex, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-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)

100 plotted points; both axes use logarithmic scales.

2icw__assembly_1__model_1 | P(r) · Pending

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 Rg	34.40 Å
Atom count	6583
Residues	809
Excluded volume	116980 Å³
Maximum q	0.500 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)

Entity 1 Entity 1 polymer

Description description	HLA class II histocompatibility antigen, DR alpha chain
Molecular weight formula_weight	20983.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	13464

EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	HLA class II histocompatibility antigen, DRB1-1 beta chain
Molecular weight formula_weight	22080.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	haemagglutinin peptide
Molecular weight formula_weight	1506.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

PKYVKQNTLKLAT

Entity 4 Entity 4 polymer

Description description	Mycoplasma arthritidis mitogen
Molecular weight formula_weight	25332.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

MKLRVENPKKAQKHFVQNLNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLSYFISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELWWFRSLLVKGVYLIKRYYEGDIELKTTSDFAKAVFED

Source Source

Source organism organism	Mycoplasma arthritidis
NCBI taxonomy ID ncbi_taxonomy_id	2111
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	T-cell receptor alpha chain V
Molecular weight formula_weight	12113.6 kDa
Mutation mutation	W82R, L43P
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K

QSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGPQLLLKYYSGDPVVQGVNGFEAEFSKSNSSFHLRKASVHRSDSAVYFCAVSGFASALTFGSGTKVIVL

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	T-cell receptor beta chain V
Molecular weight formula_weight	12184.3 kDa
Mutation mutation	G17E, G42E, L80S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,L

EAAVTQSPRNKVAVTGEKVTLSCNQTNNHNNMYWYRQDTGHELRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILESATPSQTSVYFCASGGGGTLYFGAGTRLSVLSSA

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	305

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d2icwa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2icwa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d2icwb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2icwb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d2icwd1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2icwd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d2icwe1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2icwe2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d2icwg_
Class class	a — All alpha proteins
Fold Fold fold	a.202 — Superantigen MAM
Superfamily Superfamily superfamily	a.202.1 — Superantigen MAM
Family Family family	a.202.1.1 — Superantigen MAM

Domain ID domain_id	d2icwh_
Class class	a — All alpha proteins
Fold Fold fold	a.202 — Superantigen MAM
Superfamily Superfamily superfamily	a.202.1 — Superantigen MAM
Family Family family	a.202.1.1 — Superantigen MAM

Domain ID domain_id	d2icwj1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2icwj2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2icwl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2icwl3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (16 domains)

Domain ID domain_id	2icwA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

Domain ID domain_id	2icwA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2icwB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

Domain ID domain_id	2icwB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2icwD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

Domain ID domain_id	2icwD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2icwE01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

Domain ID domain_id	2icwE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2icwG01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	390 — Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1

Domain ID domain_id	2icwG02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	530 — mam-mhc complex, Chain D, Domain 2

Domain ID domain_id	2icwH01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	390 — Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1

Domain ID domain_id	2icwH02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	530 — mam-mhc complex, Chain D, Domain 2

Domain ID domain_id	2icwI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2icwJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2icwK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2icwL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	61.516 Å
Unit-cell length b length_b	86.822 Å
Unit-cell length c length_c	116.981 Å
Unit-cell angle α angle_alpha	110.27 °
Unit-cell angle β angle_beta	92.32 °
Unit-cell angle γ angle_gamma	107.87 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.410 Å
Low-resolution limit resolution_low	47.790 Å
R factor r_factor	0.2420
R_work r_work	0.2420
R_free r_free	0.2880

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

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

HLA class II histocompatibility antigen, DR alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HLA class II histocompatibility antigen, DRB1-1 beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mycoplasma arthritidis mitogen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T-cell receptor alpha chain V

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T-cell receptor beta chain V

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2icw__assembly_1__model_1

2icw__assembly_1__model_1 | I(q)

2icw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (14 domains)

CATH v4.4 (16 domains)

7. Citations (1)