4mng

Structure of the DP10.7 TCR with CD1d-sulfatide

Method: X-RAY DIFFRACTION

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

Beta-2-microglobulin

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Cd1d1 protein × 1 （P15813,Q7TMK5） TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region × 1 （Q6PJ56） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Cd1d1 protein × 1 （P15813,Q7TMK5） TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region × 1 （Q6PJ56） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 21–119 Author chain D； PDBConstruct 1–99； UniProt 21–119

Cd1d1 protein

Mus musculus

UniProt P15813

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P01887） TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region × 1 （Q6PJ56） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P01887） TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region × 1 （Q6PJ56） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD1D_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–184； UniProt 21–201 Author chain C； PDBConstruct 4–184； UniProt 21–201

Cd1d1 protein

Mus musculus

UniProt Q7TMK5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P01887） TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region × 1 （Q6PJ56） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P01887） TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region × 1 （Q6PJ56） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7TMK5_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 185–278； UniProt 73–166 Author chain C； PDBConstruct 185–278； UniProt 73–166

TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region

Homo sapiens

UniProt Q6PJ56

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P01887） Cd1d1 protein × 1 （P15813,Q7TMK5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P01887） Cd1d1 protein × 1 （P15813,Q7TMK5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6PJ56_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–119； UniProt 21–142 Author chain F； PDBConstruct 1–119； UniProt 21–142

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	4mng
Deposition date deposition_date	2013-09-10
Structure title title	Structure of the DP10.7 TCR with CD1d-sulfatide
Keywords keywords	;Immunglobulin, Histocompatibility Antigens, CD1, Immunological, lymphocytes, gamma delta T cell, T cell recognition, self-recognition, myelin, intestinal epithelial lymphocytes, Human, Lipid binding, self-ligand, Glycoproteins, Cell-surface receptors, 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.

4mng__assembly_1__model_1

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

Download this curve (.dat)

4mng__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4mng__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.71 Å
Rg (electron density)	33.52 Å
Total Rg	33.96 Å
Atom count	4874
Residues	600
Excluded volume	86650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4mng__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4mng__assembly_2__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11660.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	9775

IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Cd1d1 protein
Molecular weight formula_weight	31972.8 kDa
Mutation mutation	human CD1d alpha3 domain replaced with mouse CD1d alpha3 domain
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ADPVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWSGR

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region
Molecular weight formula_weight	28534.9 kDa
Mutation mutation	end of gamma sequence TLVV swapped with KLII
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGEPSYWGFPRTTRVIFGKGTRVTVEPGGGGSGGGGSGGGGSGGGGSSSNLEGRTKSVIRQTGSSAEITCDLAEGSTGYIHWYLHQEGKAPQRLLYYDSYTSSVVLESGISPGKYDTYGSTRKNLRMILRNLIENDSGVYYCATWDEKYYKKLFGSGTKLIITDAASGAD

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 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	(15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE
Molecular weight formula_weight	890.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4mnga1
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	d4mnga2
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	d4mnga3
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	d4mngb_
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	d4mngc1
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	d4mngc2
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	d4mngc3
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	d4mngd_
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	d4mnge1
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.1.1.0 — automated matches

Domain ID domain_id	d4mnge2
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.1.1.0 — automated matches

Domain ID domain_id	d4mngf1
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.1.1.0 — automated matches

Domain ID domain_id	d4mngf2
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.1.1.0 — automated matches

CATH v4.4 (10 domains)

Domain ID domain_id	4mngA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	4mngA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4mngB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4mngC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	4mngC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4mngD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4mngE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4mngE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4mngF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4mngF02
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	229.333 Å
Unit-cell length b length_b	229.333 Å
Unit-cell length c length_c	52.646 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	3.006 Å
Low-resolution limit resolution_low	49.652 Å
R factor r_factor	0.1794
R_work r_work	0.1779
R_free r_free	0.2068

Structure of the DP10.7 TCR with CD1d-sulfatide

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

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cd1d1 protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cd1d1 protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region

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

4mng__assembly_1__model_1

4mng__assembly_1__model_1 | I(q)

4mng__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

CATH v4.4 (10 domains)

7. Citations (1)