SAXSdb — 8dnt

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

Nucleoprotein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 MHC class I antigen alpha chain × 1 （U5YKE0） Beta-2-microglobulin × 1 （P61769）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 MHC class I antigen alpha chain × 1 （U5YKE0） Beta-2-microglobulin × 1 （P61769）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 MHC class I antigen alpha chain × 1 （U5YKE0） Beta-2-microglobulin × 1 （P61769）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 MHC class I antigen alpha chain × 1 （U5YKE0） Beta-2-microglobulin × 1 （P61769）	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	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–9； UniProt 222–230 Author chain J； PDBConstruct 1–9； UniProt 222–230 Author chain Q； PDBConstruct 1–9； UniProt 222–230 Author chain X； PDBConstruct 1–9； UniProt 222–230

MHC class I antigen alpha chain

Homo sapiens

UniProt U5YKE0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 Nucleoprotein × 1 （P0DTC9） Beta-2-microglobulin × 1 （P61769）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 Nucleoprotein × 1 （P0DTC9） Beta-2-microglobulin × 1 （P61769）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 Nucleoprotein × 1 （P0DTC9） Beta-2-microglobulin × 1 （P61769）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 Nucleoprotein × 1 （P0DTC9） Beta-2-microglobulin × 1 （P61769）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	U5YKE0_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 2–276； UniProt 25–299 Author chain K； PDBConstruct 2–276； UniProt 25–299 Author chain R； PDBConstruct 2–276； UniProt 25–299 Author chain Y； 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	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 Nucleoprotein × 1 （P0DTC9） MHC class I antigen alpha chain × 1 （U5YKE0）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 Nucleoprotein × 1 （P0DTC9） MHC class I antigen alpha chain × 1 （U5YKE0）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 Nucleoprotein × 1 （P0DTC9） MHC class I antigen alpha chain × 1 （U5YKE0）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 Nucleoprotein × 1 （P0DTC9） MHC class I antigen alpha chain × 1 （U5YKE0）	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	5
Chains and sequence ranges	Author chain F； PDBConstruct 2–100； UniProt 21–119 Author chain L； PDBConstruct 2–100； UniProt 21–119 Author chain T； PDBConstruct 2–100； UniProt 21–119 Author chain Z； PDBConstruct 2–100； UniProt 21–119

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	8dnt
Deposition date deposition_date	2022-07-11
Structure title title	SARS-CoV-2 specific T cell receptor
Keywords keywords	TCR complex, MHC, HLA, SARS-CoV-2, 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.

8dnt__assembly_1__model_1

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

Download this curve (.dat)

8dnt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8dnt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.17 Å
Rg (electron density)	37.37 Å
Total Rg	37.51 Å
Atom count	6571
Residues	825
Excluded volume	114880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8dnt__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8dnt__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8dnt__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`8dnt__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	T-cell receptor alpha chain
Molecular weight formula_weight	22544.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,H,M,V
Atom count atom_count	26210

KEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAVREGAQKLVFGQGTRLTINPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

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	T-cell receptor beta chain
Molecular weight formula_weight	27076.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,I,P,W

GAGVSQSPSNKVTEKGKDVELRCDPISGHTALYWYRQSLGQGLEFLIYFQGNSAPDKSGLPSDRFSAERTGGSVSTLTIQRTQQEDSAVYLCASSLDLGADEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

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	Nucleoprotein
Molecular weight formula_weight	1098.3 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,J,Q,X

LLLDRLNQL

Entity 4 Entity 4 polymer

Description description	MHC class I antigen alpha chain
Molecular weight formula_weight	32156.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,K,R,Y

MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEGGG

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	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	F,L,T,Z

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

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Unit-cell length a length_a	182.158 Å
Unit-cell length b length_b	121.827 Å
Unit-cell length c length_c	210.555 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.180 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2256
R_work r_work	0.2210
R_free r_free	0.3126

SARS-CoV-2 specific T cell receptor

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

Nucleoprotein

State in the Current Structure

Other States of the Same Protein in the Database

MHC class I antigen alpha chain

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8dnt__assembly_1__model_1

8dnt__assembly_1__model_1 | I(q)

8dnt__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

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

7. Citations (1)

SARS-CoV-2 specific T cell receptor

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

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

MHC class I antigen 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8dnt__assembly_1__model_1

8dnt__assembly_1__model_1 | I(q)

8dnt__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

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

7. Citations (1)