7ndu

Gag:02 TCR in complex with HLA-E featuring a non-natural amino acid

Method: X-RAY DIFFRACTION

▼

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

HLA class I histocompatibility antigen, alpha chain E

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 （A0A075B6U7,A0A0B4J268,P0DSE1） T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 （A0A0J9YX06,K7N5M4,P04435）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLAE_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 2–277； UniProt 22–297

Beta-2-microglobulin

Homo sapiens

UniProt P61769

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, alpha chain E × 1 （P13747） Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 （A0A075B6U7,A0A0B4J268,P0DSE1） T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 （A0A0J9YX06,K7N5M4,P04435）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain BBB； PDBConstruct 2–100； UniProt 21–119

T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain

Homo sapiens

UniProt A0A075B6U7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, alpha chain E × 1 （P13747） Beta-2-microglobulin × 1 （P61769） Gag6V(276-284 H4C) × 1 T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 （A0A0J9YX06,K7N5M4,P04435）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A075B6U7_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain DDD； PDBConstruct 96–113； UniProt 4–21

T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain

Homo sapiens

UniProt A0A0B4J268

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, alpha chain E × 1 （P13747） Beta-2-microglobulin × 1 （P61769） Gag6V(276-284 H4C) × 1 T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 （A0A0J9YX06,K7N5M4,P04435）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVA4_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain DDD； PDBConstruct 2–92； UniProt 18–108

T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain

Homo sapiens

UniProt P0DSE1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, alpha chain E × 1 （P13747） Beta-2-microglobulin × 1 （P61769） Gag6V(276-284 H4C) × 1 T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 （A0A0J9YX06,K7N5M4,P04435）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRAR1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain DDD； PDBConstruct 115–199； UniProt 129–213

T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain

Homo sapiens

UniProt A0A0J9YX06

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, alpha chain E × 1 （P13747） Beta-2-microglobulin × 1 （P61769） Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 （A0A075B6U7,A0A0B4J268,P0DSE1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TJB12_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain EEE； PDBConstruct 101–114； UniProt 2–15

T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain

Homo sapiens

UniProt K7N5M4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, alpha chain E × 1 （P13747） Beta-2-microglobulin × 1 （P61769） Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 （A0A075B6U7,A0A0B4J268,P0DSE1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	K7N5M4_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain EEE； PDBConstruct 115–244； UniProt 120–249

T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain

Homo sapiens

UniProt P04435

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	HLA class I histocompatibility antigen, alpha chain E × 1 （P13747） Beta-2-microglobulin × 1 （P61769） Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 （A0A075B6U7,A0A0B4J268,P0DSE1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVB79_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain EEE； PDBConstruct 2–97； UniProt 20–115

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	7ndu
Deposition date deposition_date	2021-02-02
Structure title title	Gag:02 TCR in complex with HLA-E featuring a non-natural amino acid
Keywords keywords	TCR-pHLA complex, non-natural amino acid, 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.

7ndu__assembly_1__model_1

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

Download this curve (.dat)

7ndu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ndu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.05 Å
Rg (electron density)	37.29 Å
Total Rg	37.42 Å
Atom count	6529
Residues	809
Excluded volume	114280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ndu__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	HLA class I histocompatibility antigen, alpha chain E
Molecular weight formula_weight	31911.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA
Atom count atom_count	6545

MGSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQCAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

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	Beta-2-microglobulin
Molecular weight formula_weight	11879.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	BBB

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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	Gag6V(276-284 H4C)
Molecular weight formula_weight	1098.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	CCC

RMYSPVSIL

Entity 4 Entity 4 polymer

Description description	T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain
Molecular weight formula_weight	22074.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	DDD

MLAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEVASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGSSFNQGGKLIFGQGTELSVKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDT

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 5 Entity 5 polymer

Description description	T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain
Molecular weight formula_weight	27914.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	EEE

MDTGVSQNPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSRLLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSLGREYGYTFGSGTRLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

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

▶

Unit-cell length a length_a	88.980 Å
Unit-cell length b length_b	88.980 Å
Unit-cell length c length_c	293.570 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	61.597 Å
R factor r_factor	—
R_work r_work	0.2419
R_free r_free	0.3015

Gag:02 TCR in complex with HLA-E featuring a non-natural amino acid

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

HLA class I histocompatibility antigen, alpha chain E

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 4,T cell receptor alpha joining 23,M1-specific 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

T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific 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

T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific 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

T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr 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

T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr 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

T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr 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

7ndu__assembly_1__model_1

7ndu__assembly_1__model_1 | I(q)

7ndu__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source