SAXSdb — 8ye4

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

MHC class I antigen precusor

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） Spike protein S1 × 1 （P0DTC2） TCR NYN-I alpha chain × 1 TCR NYN-I beta chain × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） Spike protein S1 × 1 （P0DTC2） TCR NYN-I alpha chain × 1 TCR NYN-I beta chain × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6IVJ7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–274； UniProt 25–298 Author chain C； PDBConstruct 1–274； UniProt 25–298

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	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen precusor × 1 （Q6IVJ7） Spike protein S1 × 1 （P0DTC2） TCR NYN-I alpha chain × 1 TCR NYN-I beta chain × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen precusor × 1 （Q6IVJ7） Spike protein S1 × 1 （P0DTC2） TCR NYN-I alpha chain × 1 TCR NYN-I beta chain × 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 21–119 Author chain D； PDBConstruct 1–99； UniProt 21–119

Spike protein S1

OrganismNot specified

UniProt P0DTC2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen precusor × 1 （Q6IVJ7） Beta-2-microglobulin × 1 （P61769） TCR NYN-I alpha chain × 1 TCR NYN-I beta chain × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen precusor × 1 （Q6IVJ7） Beta-2-microglobulin × 1 （P61769） TCR NYN-I alpha chain × 1 TCR NYN-I beta chain × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_SARS2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–9； UniProt 448–456 Author chain F； PDBConstruct 1–9； UniProt 448–456

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	8ye4
Deposition date deposition_date	2024-02-21
Structure title title	The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF
Keywords keywords	SARS-CoV-2, TCR-pMHC complex, CD8 T cell epitope, 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.

8ye4__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8ye4__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ye4__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.13 Å
Rg (electron density)	35.26 Å
Total Rg	35.49 Å
Atom count	5923
Residues	751
Excluded volume	103510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ye4__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8ye4__assembly_2__model_1`	pentameric （5）	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	MHC class I antigen precusor
Molecular weight formula_weight	31551.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	12294

GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

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	11748.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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	Spike protein S1
Molecular weight formula_weight	1266.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

NYNYLYRLF

Entity 4 Entity 4 polymer

Description description	TCR NYN-I alpha chain
Molecular weight formula_weight	20701.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EVEQDPGPFNVPEGATVAFNCTYSNSASQSFFWYRQDCRKEPKLLMSVYSSGNEDGRFTAQLNRASQYISLLIRDSKLSDSATYLCVVNAHSGAGSYQLTFGKGTKLSVIPIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAF

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	TCR NYN-I beta chain
Molecular weight formula_weight	26851.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSETGGYEQYFGPGTRLTVTDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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Unit-cell length a length_a	69.002 Å
Unit-cell length b length_b	148.096 Å
Unit-cell length c length_c	196.213 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	39.980 Å
R factor r_factor	0.2681
R_work r_work	0.2659
R_free r_free	0.3098

The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF

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

MHC class I antigen precusor

State in the Current Structure

Other States of the Same Protein in the Database

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Spike protein S1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8ye4__assembly_2__model_1

8ye4__assembly_2__model_1 | I(q)

8ye4__assembly_2__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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 water

7. Citations (1)

The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF

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

MHC class I antigen precusor

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

Spike protein S1

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

8ye4__assembly_2__model_1

8ye4__assembly_2__model_1 | I(q)

8ye4__assembly_2__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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 water

7. Citations (1)