8t4z

T-cell receptor and lipid complex structure

Method: X-RAY DIFFRACTION

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

Antigen-presenting glycoprotein CD1d1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 其他Polymer 3	Beta-2-microglobulin × 1 （P01887） T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera × 1 （A0A0B4J1J9,K7N5M3） Beta-chain, T cell receptor beta chain MC.7.G5 chimera × 1 （A2NTY6,P0DTU4） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD1D1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–279； UniProt 19–297

Beta-2-microglobulin

Mus musculus

UniProt P01887

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 其他Polymer 3	Antigen-presenting glycoprotein CD1d1 × 1 （P11609） T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera × 1 （A0A0B4J1J9,K7N5M3） Beta-chain, T cell receptor beta chain MC.7.G5 chimera × 1 （A2NTY6,P0DTU4） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1 water × 4	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 21–119

T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera

Homo sapiens

UniProt A0A0B4J1J9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 其他Polymer 3	Antigen-presenting glycoprotein CD1d1 × 1 （P11609） Beta-2-microglobulin × 1 （P01887） Beta-chain, T cell receptor beta chain MC.7.G5 chimera × 1 （A2NTY6,P0DTU4） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0B4J1J9_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–92； UniProt 23–114

T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera

Homo sapiens

UniProt K7N5M3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 其他Polymer 3	Antigen-presenting glycoprotein CD1d1 × 1 （P11609） Beta-2-microglobulin × 1 （P01887） Beta-chain, T cell receptor beta chain MC.7.G5 chimera × 1 （A2NTY6,P0DTU4） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	K7N5M3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 113–207； UniProt 116–210

Beta-chain, T cell receptor beta chain MC.7.G5 chimera

Mus musculus

UniProt A2NTY6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 其他Polymer 3	Antigen-presenting glycoprotein CD1d1 × 1 （P11609） Beta-2-microglobulin × 1 （P01887） T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera × 1 （A0A0B4J1J9,K7N5M3） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A2NTY6_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–95； UniProt 29–123

Beta-chain, T cell receptor beta chain MC.7.G5 chimera

Mus musculus

UniProt P0DTU4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 其他Polymer 3	Antigen-presenting glycoprotein CD1d1 × 1 （P11609） Beta-2-microglobulin × 1 （P01887） T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera × 1 （A0A0B4J1J9,K7N5M3） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRBR2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 100–242； UniProt 124–266

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	8t4z
Deposition date deposition_date	2023-06-12
Structure title title	T-cell receptor and lipid complex structure
Keywords keywords	MHC-like protein, lipid binding protein, antigen-presenting molecule; LIPID BINDING PROTEIN
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.

8t4z__assembly_1__model_1

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

Download this curve (.dat)

8t4z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8t4z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.43 Å
Rg (electron density)	40.73 Å
Total Rg	40.61 Å
Atom count	6623
Residues	835
Excluded volume	116630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8t4z__assembly_1__model_1`	tetrameric （4）	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 (8)

Entity 1 Entity 1 polymer

Description description	Antigen-presenting glycoprotein CD1d1
Molecular weight formula_weight	34662.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6649

SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHHHH

Source Source

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

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11660.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Source Source

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

Entity 3 Entity 3 polymer

Description description	T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera
Molecular weight formula_weight	22779.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

TQVEQSPQSLVVRQGENSVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

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 polymer

Description description	Beta-chain, T cell receptor beta chain MC.7.G5 chimera
Molecular weight formula_weight	27114.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

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

Entity 5 Entity 5 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide
Molecular weight formula_weight	648.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

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Unit-cell length a length_a	57.906 Å
Unit-cell length b length_b	79.036 Å
Unit-cell length c length_c	242.373 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.691 Å
Low-resolution limit resolution_low	48.087 Å
R factor r_factor	0.1966
R_work r_work	0.1929
R_free r_free	0.2654

T-cell receptor and lipid complex structure

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

Antigen-presenting glycoprotein CD1d1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera

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 variable 11, Human nkt tcr alpha chain chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-chain, T cell receptor beta chain MC.7.G5 chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-chain, T cell receptor beta chain MC.7.G5 chimera

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

8t4z__assembly_1__model_1

8t4z__assembly_1__model_1 | I(q)

8t4z__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 (8)

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 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)