8ybn

Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB)

Method: X-RAY DIFFRACTION D_max: 84.9 Å Quality: REASONABLE

▼

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

Enterotoxin type B

Staphylococcus aureus

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 28–266	Not recorded	nanobody SEB-Nb8 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000	Resolution 2.18 Å R-free 0.281

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 8YBN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D5M X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDE AND SEB Deposited 1999-10-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–266（239 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；5% PEG 4000, 0.01 M NA ACETATE, PH 5, 2.4% ETHYLENE GLYCOL, pH 7.4	Resolution 2.00 Å R-free 0.260
1D5X X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH DIPEPTIDE MIMETIC AND SEB Deposited 1999-10-12	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.45 Å R-free 0.268
1D5Z X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDOMIMETIC AND SEB Deposited 1999-10-12	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.00 Å R-free 0.265
1D6E CRYSTAL STRUCTURE OF HLA-DR4 COMPLEX WITH PEPTIDOMIMETIC AND SEB Deposited 1999-10-13	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5	Resolution 2.45 Å R-free 0.226
1GOZ Structural basis for the altered T-cell receptor binding specificty in a superantigenic staphylococcus aureus Enterotoxin-B mutant Deposited 2001-10-29	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–266（239 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PH 4.6 SODIUM CITRATE BUFFER, 0.1M AMMONIUM ACETATE	Resolution 2.00 Å R-free 0.246
1GOZ Structural basis for the altered T-cell receptor binding specificty in a superantigenic staphylococcus aureus Enterotoxin-B mutant Deposited 2001-10-29	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–266（239 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PH 4.6 SODIUM CITRATE BUFFER, 0.1M AMMONIUM ACETATE	Resolution 2.00 Å R-free 0.246
1SBB T-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SUPERANTIGEN SEB Deposited 1999-02-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 28–266（239 aa） Chain D 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；CRYSTALLIZATION CONDITIONS: 10% PEG 8000 0.1M TRIS-HCL, PH8.5	Resolution 2.40 Å R-free 0.309
1SE3 STAPHYLOCOCCAL ENTEROTOXIN B COMPLEXED WITH GM3 TRISACCHARIDE Deposited 1996-10-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.8；24% PEG 4000, 20 MM BORATE BUFFER AT PH 8.8.	Resolution 2.30 Å R-free 0.330
1SE4 STAPHYLOCOCCAL ENTEROTOXIN B COMPLEXED WITH LACTOSE Deposited 1997-04-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.8；CRYSTALLIZED FROM 24% PEG 4000, 20 MM BORATE BUFFER AT PH 8.8 IN THE PRESENCE OF 100MM LACTOSE	Resolution 1.90 Å
1SEB COMPLEX OF THE HUMAN MHC CLASS II GLYCOPROTEIN HLA-DR1 AND THE BACTERIAL SUPERANTIGEN SEB Deposited 1995-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 29–262（234 aa） Chain H 29–262（234 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å R-free 0.327
2SEB X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH A PEPTIDE FROM HUMAN COLLAGEN II Deposited 1997-10-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 28–266（239 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1 M NA ACETATE PH 4.6 9 - 14% PEG 4000 0.2 M AMMONIUM ACETATE	Resolution 2.50 Å R-free 0.280
3GP7 Staphylococcal Enterotoxin B mutant N23YK97SK98S Deposited 2009-03-23	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–266（239 aa）	Mutation：N23Y, K97S, K98S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18% (w/v) PEG 3350, 0.02% Na azide, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.224
3GP7 Staphylococcal Enterotoxin B mutant N23YK97SK98S Deposited 2009-03-23	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–266（239 aa）	Mutation：N23Y, K97S, K98S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18% (w/v) PEG 3350, 0.02% Na azide, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.224
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 3 SO4 SULFATE ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 3 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 28–266（239 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 3 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 2 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3SEB STAPHYLOCOCCAL ENTEROTOXIN B Deposited 1997-11-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–265（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.48 Å
3W2D Crystal Structure of Staphylococcal Eenterotoxin B in complex with a novel neutralization monoclonal antibody Fab fragment Deposited 2012-11-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–266（239 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å R-free 0.261
4RGM Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 20B1 Deposited 2014-09-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES sodium, pH 7.5, 20% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.69 Å R-free 0.277
4RGM Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 20B1 Deposited 2014-09-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES sodium, pH 7.5, 20% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.69 Å R-free 0.277
4RGN Structure of Staphylococcal Enterotoxin B bound to two neutralizing antibodies, 14G8 and 6D3 Deposited 2014-09-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；0.1 M phosphate/citrate, pH 4.2, 6.7% w/v PEG3000, 0.5 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.278
4RGN Structure of Staphylococcal Enterotoxin B bound to two neutralizing antibodies, 14G8 and 6D3 Deposited 2014-09-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；0.1 M phosphate/citrate, pH 4.2, 6.7% w/v PEG3000, 0.5 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.278
4RGO Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 14G8 Deposited 2014-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；80 mM sodium cacodylate, pH 6.5, 16% w/v PEG8000, 160 mM magnesium acetate, 20% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.189
8YBL Crystal structure of nanobody SEB-Nb3 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3,350	Resolution 2.33 Å R-free 0.262
8YBM Crystal structure of nanobody SEB-Nb6 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；2% v/v 1,4-Dioxane, 0.1 M Tris pH 8.0, 15% w/v Polyethylene glycol 3,350	Resolution 2.04 Å R-free 0.259
8YBM Crystal structure of nanobody SEB-Nb6 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；2% v/v 1,4-Dioxane, 0.1 M Tris pH 8.0, 15% w/v Polyethylene glycol 3,350	Resolution 2.04 Å R-free 0.259
8YBO Crystal structure of nanobody SEB-Nb11 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350	Resolution 1.59 Å R-free 0.284
8YBO Crystal structure of nanobody SEB-Nb11 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350	Resolution 1.59 Å R-free 0.284
8YBP Crystal structure of nanobody SEB-Nb20 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v Polyethylene glycol 3,350	Resolution 2.08 Å R-free 0.253
8YKT Fab and SEB complex Deposited 2024-03-05	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithum sulfate, 0.1M Sodium acetate pH5.5, 10%PEG1000, 10% PEG8000	Resolution 2.04 Å R-free 0.230

22 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ETXB_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–240； UniProt 28–266

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ybn
Deposition date deposition_date	2024-02-15
最后修订 last_revision	2024-12-25
Structure title title	Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB)
Keywords keywords	antibody, nanobody, toxin, staphylococcal enterotoxin B (SEB), antitoxin; ANTITOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.63 Å
Radius of gyration Rg (electron density) rg_electron	23.95 Å
Forward intensity I(0) i0	29277700.00
Molecular weight molecular_weight	41372.0 kDa
Excluded volume excluded_volume	51604 Å³
Envelope volume envelope_volume	62546 Å³
Hydration-shell volume shell_volume	22801 Å³
Envelope diameter envelope_diameter	85.2 Å
Shell Rg shell_rg	29.59 Å
Envelope Rg envelope_rg	24.19 Å
Shape Rg shape_rg	23.91 Å
Total Rg total_rg	24.72 Å
Total atoms total_atoms	2915
Residues n_residues	358
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

▼

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

Maximum dimension Dmax dmax	84.9 Å
Rg (real space) rg_real	24.77 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	2.9280e+07
I(0) uncertainty (real space) i0_real_error	4.1020e+05
Rg (reciprocal space) rg_reciprocal	24.74 Å
I(0) (reciprocal space) i0_reciprocal	29280000.0000
Solution quality estimate total_estimate	0.6260
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.475
Kurtosis Kurtosis kurtosis	-0.272
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8471000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 0.991; Sysdev: 0.338; Positv: 1.000; Valcen: 0.817; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Enterotoxin type B
Molecular weight formula_weight	28542.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2975

MESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	nanobody SEB-Nb8
Molecular weight formula_weight	14428.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLVESGGGSVQDGGSLRLSCAASGFTIDNRWMTWFRQAPGKEREGVASILTYSGRTVYADSGKGRFTISQANAKNSVYLQMNSLKPEDTATYYCAAGDAYHKWFMPSSRALDRKEYNYWGQGTLVTVSS

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

▶

8. Citations (1)

▶

Unit-cell length a length_a	44.967 Å
Unit-cell length b length_b	87.860 Å
Unit-cell length c length_c	95.581 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	64.680 Å
R factor r_factor	0.2346
R_work r_work	0.2322
R_free r_free	0.2808

fit	/app/data/saxs_computation/yb/8ybn/8ybn.fit
pddf	/app/data/pr_computation/yb/8ybn/8ybn.pr.out
profile	/app/data/saxs_computation/yb/8ybn/8ybn.dat

Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB)

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

Enterotoxin type B

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)