1lo5

Crystal structure of the D227A variant of Staphylococcal enterotoxin A in complex with human MHC class II

Method: X-RAY DIFFRACTION Dmax: 101.7 Å Quality: GOOD

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

HLA class II histocompatibility antigen, DR alpha chain

Homo sapiens

UniProt P01903

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 26–207 Fragment:extracellular domain HLA class II histocompatibility antigen, DR-1 beta chain × 1 (P04229) Hemagglutinin peptide × 1 enterotoxin A × 1 (P0A0L2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.2M (NH4)2SO4, 0.1M MES, 24%(w/v) polyethylen glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.20 Å R-free 0.339

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.

139 other PDB entries and 219 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 2DRA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–182; UniProt 26–207

HLA class II histocompatibility antigen, DR-1 beta chain

Homo sapiens

UniProt P04229

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 30–219 Fragment:extracellular domain HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) Hemagglutinin peptide × 1 enterotoxin A × 1 (P0A0L2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.2M (NH4)2SO4, 0.1M MES, 24%(w/v) polyethylen glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.20 Å R-free 0.339

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.

48 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 2B11_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–190; UniProt 30–219

enterotoxin A

Staphylococcus aureus

UniProt P0A0L2

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 25–257 Mutation:D227A HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DR-1 beta chain × 1 (P04229) Hemagglutinin peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.2M (NH4)2SO4, 0.1M MES, 24%(w/v) polyethylen glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.20 Å R-free 0.339

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.

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ETXA_STAAU
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–233; UniProt 25–257

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

SAXS profile for 1lo5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1lo5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1lo5
Deposition date deposition_date2002-05-06
Structure title titleCrystal structure of the D227A variant of Staphylococcal enterotoxin A in complex with human MHC class II
Keywords keywordsPROTEIN-PROTEIN COMPLEX, IMMUNE SYSTEM-Toxin COMPLEX; IMMUNE SYSTEM/Toxin
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.06
Radius of gyration Rg (electron density) rg_electron30.45
Forward intensity I(0) i080866600.00
Molecular weight molecular_weight71184.0 kDa
Excluded volume excluded_volume89045 ų
Envelope volume envelope_volume114140 ų
Hydration-shell volume shell_volume32280 ų
Envelope diameter envelope_diameter107.3
Shell Rg shell_rg36.33
Envelope Rg envelope_rg30.55
Shape Rg shape_rg30.42
Total Rg total_rg31.08
Total atoms total_atoms5032
Residues n_residues613
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax101.7
Rg (real space) rg_real31.15
Rg uncertainty (real space) rg_real_error0.95
I(0) (real space) i0_real8.0870e+07
I(0) uncertainty (real space) i0_real_error1.3290e+06
Rg (reciprocal space) rg_reciprocal31.11
I(0) (reciprocal space) i0_reciprocal80860000.0000
Solution quality estimate total_estimate0.8743
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary99.7
Skewness Skewness skewness0.393
Kurtosis Kurtosis kurtosis-0.334
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11480000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.921; Smooth: 0.717

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1lo5a1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1lo5a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1lo5b1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1lo5b2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1lo5d1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.2 — Superantigen toxins, N-terminal domain
Domain ID domain_idd1lo5d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.6 — Superantigen toxins, C-terminal domain
Family Family familyd.15.6.1 — Superantigen toxins, C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id1lo5A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1lo5A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1lo5B01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id1lo5B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1lo5D01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id1lo5D02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily120

8. Citations (1)

9. Files and Curves (10)