1l0x

TCR beta chain complexed with streptococcal superantigen SpeA

Method: X-RAY DIFFRACTION D_max: 123.3 Å Quality: GOOD

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

14.3.d T cell receptor beta chain

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 32–267	Mutation：N24Q, N74Q, N121Q	Exotoxin type A × 1 （P08095） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG8000, 0.2M MgCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 32–267	Mutation：N24Q, N74Q, N121Q	Exotoxin type A × 1 （P08095） GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG8000, 0.2M MgCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1L0X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L0Y T cell receptor beta chain complexed with superantigen SpeA soaked with zinc Deposited 2002-02-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 32–265（234 aa）	Mutation：N24Q, N74Q, N121Q	ZN ZINC ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG8K, MgCl, Tris, pH 8., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
1L0Y T cell receptor beta chain complexed with superantigen SpeA soaked with zinc Deposited 2002-02-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 32–265（234 aa）	Mutation：N24Q, N74Q, N121Q	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG8K, MgCl, Tris, pH 8., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
5M01 Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from LCMV Deposited 2016-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 1–127（127 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；280 K；19% PEG 6000, 0.1M Tris HCl pH 8.0	Resolution 1.95 Å R-free 0.229
5M02 Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV Deposited 2016-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 1–127（127 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 6000, 0.1M Tris HCl pH 8.0	Resolution 1.75 Å R-free 0.214

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TCB2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–238； UniProt 32–267 Author chain C； PDBConstruct 1–238； UniProt 32–267

Exotoxin type A

Streptococcus pyogenes

UniProt P08095

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 31–251	Mutation：C90S	14.3.d T cell receptor beta chain × 1 （P01851） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG8000, 0.2M MgCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 31–251	Mutation：C90S	14.3.d T cell receptor beta chain × 1 （P01851） GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG8000, 0.2M MgCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1L0X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HA5 Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition. Deposited 2001-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–250（218 aa） Fragment：RESIDUES 33-250	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.82 Å R-free 0.283
1HA5 Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition. Deposited 2001-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 33–250（218 aa） Fragment：RESIDUES 33-250	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.82 Å R-free 0.283
1HA5 Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition. Deposited 2001-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 33–250（218 aa） Fragment：RESIDUES 33-250	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.82 Å R-free 0.283
1HA5 Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition. Deposited 2001-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 33–250（218 aa） Fragment：RESIDUES 33-250	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.82 Å R-free 0.283
1L0Y T cell receptor beta chain complexed with superantigen SpeA soaked with zinc Deposited 2002-02-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 31–251（221 aa）	Mutation：C90S	ZN ZINC ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG8K, MgCl, Tris, pH 8., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
1L0Y T cell receptor beta chain complexed with superantigen SpeA soaked with zinc Deposited 2002-02-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 31–251（221 aa）	Mutation：C90S	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG8K, MgCl, Tris, pH 8., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
1UUP Crystal Structure of A Dimeric Form of Streptococcal Pyrogenic Exotoxin A (SpeA1). Deposited 2004-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–251（221 aa） Fragment：RESIDUES 31-251 Chain D 31–251（221 aa） Fragment：RESIDUES 31-251	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.282
1UUP Crystal Structure of A Dimeric Form of Streptococcal Pyrogenic Exotoxin A (SpeA1). Deposited 2004-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 31–251（221 aa） Fragment：RESIDUES 31-251 Chain C 31–251（221 aa） Fragment：RESIDUES 31-251	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.282

3 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPEA_STRPY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–221； UniProt 31–251 Author chain D； PDBConstruct 1–221； UniProt 31–251

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1l0x
Deposition date deposition_date	2002-02-14
Structure title title	TCR beta chain complexed with streptococcal superantigen SpeA
Keywords keywords	TCR, superantigen, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.78 Å
Radius of gyration Rg (electron density) rg_electron	35.92 Å
Forward intensity I(0) i0	163103000.00
Molecular weight molecular_weight	101040.0 kDa
Excluded volume excluded_volume	125510 Å³
Envelope volume envelope_volume	163490 Å³
Hydration-shell volume shell_volume	39992 Å³
Envelope diameter envelope_diameter	127.1 Å
Shell Rg shell_rg	39.87 Å
Envelope Rg envelope_rg	35.57 Å
Shape Rg shape_rg	35.89 Å
Total Rg total_rg	36.27 Å
Total atoms total_atoms	7142
Residues n_residues	914
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	123.3 Å
Rg (real space) rg_real	35.97 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	1.6310e+08
I(0) uncertainty (real space) i0_real_error	2.9430e+06
Rg (reciprocal space) rg_reciprocal	35.85 Å
I(0) (reciprocal space) i0_reciprocal	163100000.0000
Solution quality estimate total_estimate	0.8573
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.4 Å
Skewness Skewness skewness	0.471
Kurtosis Kurtosis kurtosis	-0.303
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15670000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.805

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	14.3.d T cell receptor beta chain
Molecular weight formula_weight	26568.5 kDa
Mutation mutation	N24Q, N74Q, N121Q
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	7323

AVTQSPRNKVAVTGGKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQEQFSLILELATPSQTSVYFCASGGGRGSYAEQFFGPGTRLTVLEDLRQVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRAD

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 2 Entity 2 polymer

Description description	Exotoxin type A
Molecular weight formula_weight	25803.9 kDa
Mutation mutation	C90S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QQDPDPSQLHRSSLVKNLQNIYFLYEGDPVTHENVKSVDQLLSHDLIYNVSGPNYDKLKTELKNQEMATLFKDKNVDIYGVEYYHLCYLSENAERSACIYGGVTNHEGNHLEIPKKIVVKVSIDGIQSLSFDIETNKKMVTAQELDYKVRKYLTDNKQLYTNGPSKYETGYIKFIPKNKESFWFDFFPEPEFTQSKYLMIYKDNETLDSNTSQIEVYLTTK

来源 Source

来源生物 organism	Streptococcus pyogenes
NCBI Class编号 ncbi_taxonomy_id	1314
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1l0xa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1l0xa2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1l0xb1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.2 — Superantigen toxins, N-terminal domain

Domain ID domain_id	d1l0xb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.6 — Superantigen toxins, C-terminal domain
Family Family family	d.15.6.1 — Superantigen toxins, C-terminal domain

Domain ID domain_id	d1l0xc1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1l0xc2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1l0xd1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.2 — Superantigen toxins, N-terminal domain

Domain ID domain_id	d1l0xd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.6 — Superantigen toxins, C-terminal domain
Family Family family	d.15.6.1 — Superantigen toxins, C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1l0xA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1l0xA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1l0xB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1l0xB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1l0xC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1l0xC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1l0xD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1l0xD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

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8. Citations (1)

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Unit-cell length a length_a	71.400 Å
Unit-cell length b length_b	83.250 Å
Unit-cell length c length_c	93.583 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	40.780 Å
R factor r_factor	—
R_work r_work	0.2320
R_free r_free	0.2780

fit	/app/data/saxs_computation/l0/1l0x/1l0x.fit
pddf	/app/data/pr_computation/l0/1l0x/1l0x.pr.out
profile	/app/data/saxs_computation/l0/1l0x/1l0x.dat

TCR beta chain complexed with streptococcal superantigen SpeA

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

14.3.d T cell receptor beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Exotoxin type A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)