9wbd

Crystal structure of HLA-B*07:02 in complex with SPR epitope and Q04 TCR

Method: X-RAY DIFFRACTION

▼

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

T cell receptor alpha variable 25,T cell receptor alpha chain constant

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	TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 5	TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
3	Insufficient information	Heteromer	Protein 5	TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count
4	Insufficient information	Heteromer	Protein 5	TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVA25_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–92； UniProt 19–109 Author chain F； PDBConstruct 2–92； UniProt 19–109 Author chain K； PDBConstruct 2–92； UniProt 19–109 Author chain P； PDBConstruct 2–92； UniProt 19–109

T cell receptor alpha variable 25,T cell receptor alpha chain constant

Homo sapiens

UniProt P01848

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 5	TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
3	Insufficient information	Heteromer	Protein 5	TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count
4	Insufficient information	Heteromer	Protein 5	TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRAC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 114–206； UniProt 1–93 Author chain F； PDBConstruct 114–206； UniProt 1–93 Author chain K； PDBConstruct 114–206； UniProt 1–93 Author chain P； PDBConstruct 114–206； UniProt 1–93

HLA class I histocompatibility antigen, B alpha chain

Homo sapiens

UniProt P01889

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
3	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count
4	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 Beta-2-microglobulin × 1 （P61769） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLAB_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 2–276； UniProt 25–299 Author chain H； PDBConstruct 2–276； UniProt 25–299 Author chain M； PDBConstruct 2–276； UniProt 25–299 Author chain R； PDBConstruct 2–276； UniProt 25–299

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	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Nucleoprotein × 1 （P0DTC9） DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
3	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	Consistent with protein count
4	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Nucleoprotein × 1 （P0DTC9） GLYCEROL × 1 water × 1	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	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–100； UniProt 21–119 Author chain I； PDBConstruct 2–100； UniProt 21–119 Author chain N； PDBConstruct 2–100； UniProt 21–119 Author chain S； PDBConstruct 2–100； UniProt 21–119

Nucleoprotein

OrganismNot specified

UniProt P0DTC9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） GLYCEROL × 1 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
3	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） GLYCEROL × 1 water × 1	Consistent with protein count
4	Insufficient information	Heteromer	Protein 5	T cell receptor alpha variable 25,T cell receptor alpha chain constant × 1 （A0A0B4J276,P01848） TCR beta × 1 HLA class I histocompatibility antigen, B alpha chain × 1 （P01889） Beta-2-microglobulin × 1 （P61769） GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCAP_SARS2
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–9； UniProt 105–113 Author chain J； PDBConstruct 1–9； UniProt 105–113 Author chain O； PDBConstruct 1–9； UniProt 105–113 Author chain T； PDBConstruct 1–9； UniProt 105–113

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	9wbd
Deposition date deposition_date	2025-08-13
Structure title title	Crystal structure of HLA-B*07:02 in complex with SPR epitope and Q04 TCR
Keywords keywords	pMHC-TCR 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.

9wbd__assembly_1__model_1

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

Download this curve (.dat)

9wbd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9wbd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.25 Å
Rg (electron density)	36.51 Å
Total Rg	36.69 Å
Atom count	6343
Residues	813
Excluded volume	111010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9wbd__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9wbd__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9wbd__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9wbd__assembly_4__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 (8)

Entity 1 Entity 1 polymer

Description description	T cell receptor alpha variable 25,T cell receptor alpha chain constant
Molecular weight formula_weight	23105.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F,K,P
Atom count atom_count	25365

MGQQVMQIPQYQHVQEGEDFTTYCNSSTTLSNIQWYKQRPGGHPVFLIQLVKSGEVKKQKRLTFQFGEAKKNSSLHITATQTTDVGTYFCAGYTSGTYKYIFGTGTRLKVLANIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	TCR beta
Molecular weight formula_weight	27205.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G,L,Q

MGAGVSQSPRYKVAKRGQDVALRCDPISGHVSLFWYQQALGQGPEFLTYFQNEAQLDKSGLPSDRFFAERPEGSVSTLKIQRTQQEDSAVYLCASSLGQGHFTFGSGTRLTVVEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	HLA class I histocompatibility antigen, B alpha chain
Molecular weight formula_weight	32093.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H,M,R

MGSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHDQYAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGECVEWLRRYLENGKDKLERADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE

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 BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11879.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I,N,S

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 BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Nucleoprotein
Molecular weight formula_weight	1295.5 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J,O,T

SPRWYFYYL

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 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	14

▶

Unit-cell length a length_a	88.786 Å
Unit-cell length b length_b	102.564 Å
Unit-cell length c length_c	120.701 Å
Unit-cell angle α angle_alpha	84.14 °
Unit-cell angle β angle_beta	68.60 °
Unit-cell angle γ angle_gamma	81.10 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	48.520 Å
R factor r_factor	0.2205
R_work r_work	0.2179
R_free r_free	0.2700

Crystal structure of HLA-B*07:02 in complex with SPR epitope and Q04 TCR

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

T cell receptor alpha variable 25,T cell receptor alpha chain constant

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 25,T cell receptor alpha chain constant

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 I histocompatibility antigen, B 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

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

Nucleoprotein

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

9wbd__assembly_1__model_1

9wbd__assembly_1__model_1 | I(q)

9wbd__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 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)