1u3h

Crystal structure of mouse TCR 172.10 complexed with MHC class II I-Au molecule at 2.4 A

Method: X-RAY DIFFRACTION

▼

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

T-cell receptor alpha-chain

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Mouse TCRVbeta 172.10, extracellular variable domain × 1 （P04213） H-2 class II histocompatibility antigen, A-U alpha chain × 1 （P14438） H-2 class II histocompatibility antigen, A-U beta chain × 1 （P06344） Myelin basic protein (MBP)-peptide × 1 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Mouse TCRVbeta 172.10, extracellular variable domain × 1 （P04213） H-2 class II histocompatibility antigen, A-U alpha chain × 1 （P14438） H-2 class II histocompatibility antigen, A-U beta chain × 1 （P06344） Myelin basic protein (MBP)-peptide × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5R1B3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–105； UniProt 30–120 Author chain E； PDBConstruct 1–105； UniProt 30–120

Mouse TCRVbeta 172.10, extracellular variable domain

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 5	T-cell receptor alpha-chain × 1 （Q5R1B3） H-2 class II histocompatibility antigen, A-U alpha chain × 1 （P14438） H-2 class II histocompatibility antigen, A-U beta chain × 1 （P06344） Myelin basic protein (MBP)-peptide × 1 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha-chain × 1 （Q5R1B3） H-2 class II histocompatibility antigen, A-U alpha chain × 1 （P14438） H-2 class II histocompatibility antigen, A-U beta chain × 1 （P06344） Myelin basic protein (MBP)-peptide × 1 water × 5	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–111； UniProt 11–122 Author chain F； PDBConstruct 1–111； UniProt 11–122

H-2 class II histocompatibility antigen, A-U alpha chain

Mus musculus

UniProt P14438

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha-chain × 1 （Q5R1B3） Mouse TCRVbeta 172.10, extracellular variable domain × 1 （P04213） H-2 class II histocompatibility antigen, A-U beta chain × 1 （P06344） Myelin basic protein (MBP)-peptide × 1 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha-chain × 1 （Q5R1B3） Mouse TCRVbeta 172.10, extracellular variable domain × 1 （P04213） H-2 class II histocompatibility antigen, A-U beta chain × 1 （P06344） Myelin basic protein (MBP)-peptide × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HA2U_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–182； UniProt 1–179 Author chain G； PDBConstruct 4–182； UniProt 1–179

H-2 class II histocompatibility antigen, A-U beta chain

Mus musculus

UniProt P06344

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha-chain × 1 （Q5R1B3） Mouse TCRVbeta 172.10, extracellular variable domain × 1 （P04213） H-2 class II histocompatibility antigen, A-U alpha chain × 1 （P14438） Myelin basic protein (MBP)-peptide × 1 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha-chain × 1 （Q5R1B3） Mouse TCRVbeta 172.10, extracellular variable domain × 1 （P04213） H-2 class II histocompatibility antigen, A-U alpha chain × 1 （P14438） Myelin basic protein (MBP)-peptide × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HB2U_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–188； UniProt 28–216 Author chain H； PDBConstruct 1–188； UniProt 28–216

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_id	1u3h
Deposition date deposition_date	2004-07-21
Structure title title	Crystal structure of mouse TCR 172.10 complexed with MHC class II I-Au molecule at 2.4 A
Keywords keywords	complex, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-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.

1u3h__assembly_1__model_1

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

Download this curve (.dat)

1u3h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1u3h__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	29.93 Å
Rg (electron density)	29.64 Å
Total Rg	30.29 Å
Atom count	4863
Residues	604
Excluded volume	85504 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1u3h__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1u3h__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	T-cell receptor alpha-chain
Molecular weight formula_weight	12290.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	9909

QVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSDKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAASANSGTYQRFGTGTKLQVVP

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

Entity 2 Entity 2 polymer

Description description	Mouse TCRVbeta 172.10, extracellular variable domain
Molecular weight formula_weight	12112.2 kDa
Mutation mutation	G17E,H47Y,I75T,L78S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AVTQSPRNKVAVTGEKVTLSCNQTNNHNNMYWYRQDTGHGLRLIYYSYGAGSTEKGDIPDGYKASRPSQENFSLTLESATPSQTSVYFCASGDAGGGYEQYFGPGTRLTVL

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

Entity 3 Entity 3 polymer

Description description	H-2 class II histocompatibility antigen, A-U alpha chain
Molecular weight formula_weight	20670.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

IEADHVGSYGIVVYQSPGDIGQYTFEFDGDELFYVDLDKKETIWMLPEFAQLRSFDPQGGLQNIATGKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPE

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Drosophila melanogaster

Entity 4 Entity 4 polymer

Description description	H-2 class II histocompatibility antigen, A-U beta chain
Molecular weight formula_weight	22495.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GDSERHFVVQFQPFCYFTNGTQRIRYVTRYIYNREEYLRFDSDVGEYRAVTELGRPDAEYYNKQYLERTRAELDTVCRYNYEETEVPTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Drosophila melanogaster

Entity 5 Entity 5 polymer

Description description	Myelin basic protein (MBP)-peptide
Molecular weight formula_weight	1295.4 kDa
Mutation mutation	K4Y
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

SRGGASQYRPSQ

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	183

▼

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d1u3ha1
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	d1u3hb1
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	d1u3hc1
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	d1u3hc2
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	d1u3hc3
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	d1u3hd1
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	d1u3hd2
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	d1u3he_
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	d1u3hf_
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	d1u3hg1
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	d1u3hg2
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	d1u3hg3
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	d1u3hh1
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	d1u3hh2
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

CATH v4.4 (12 domains)

Domain ID domain_id	1u3hA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1u3hB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1u3hC01
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	1u3hC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1u3hD01
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	1u3hD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1u3hE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1u3hF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1u3hG01
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	1u3hG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1u3hH01
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	1u3hH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

Unit-cell length a length_a	87.835 Å
Unit-cell length b length_b	327.162 Å
Unit-cell length c length_c	127.161 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.420 Å
Low-resolution limit resolution_low	41.510 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2740

Crystal structure of mouse TCR 172.10 complexed with MHC class II I-Au molecule at 2.4 A

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

T-cell receptor 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

Mouse TCRVbeta 172.10, extracellular variable domain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H-2 class II histocompatibility antigen, A-U 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

H-2 class II histocompatibility antigen, A-U 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1u3h__assembly_1__model_1

1u3h__assembly_1__model_1 | I(q)

1u3h__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 (6)

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. Citations (1)