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4lxr

Structure of the Toll - Spatzle complex, a molecular hub in Drosophila development and innate immunity

Method: X-RAY DIFFRACTION Dmax: 150.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein toll

Drosophila melanogaster

UniProt P08953

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 3 其他Polymer 4 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 28–802 Fragment：UNP residues 28-802 Protein spaetzle C-106 × 2 （P48607） ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；10% PEG 3350, 50 mM HEPES-Na salt, pH 7.5, vapor diffusion, hanging drop, temperature 287K Resolution 2.20 Å R-free 0.218

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 4LXR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4ARN Crystal structure of the N-terminal domain of Drosophila Toll receptor Deposited 2012-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–228（201 aa） Fragment：TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7
Resolution 2.41 Å R-free 0.216
4ARN Crystal structure of the N-terminal domain of Drosophila Toll receptor Deposited 2012-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–228（201 aa） Fragment：TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7
Resolution 2.41 Å R-free 0.216
4ARN Crystal structure of the N-terminal domain of Drosophila Toll receptor Deposited 2012-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 28–228（201 aa） Fragment：TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7
Resolution 2.41 Å R-free 0.216
4ARN Crystal structure of the N-terminal domain of Drosophila Toll receptor Deposited 2012-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain D 28–228（201 aa） Fragment：TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7
Resolution 2.41 Å R-free 0.216
4ARR Crystal structure of the N-terminal domain of Drosophila Toll receptor with the magic triangle I3C Deposited 2012-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–228（201 aa） Fragment：TOLL RECEPTOR (UNP RESIDUES 28-228), VARIABLE LYMPHOCYTE RECEPTOR B.61 (UNP RESIDUES 133-201)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；SODIUM MALONATE AND 5-AMINO-2,4, 6-TRIIODOISOPHTHALIC ACID, pH 7
Resolution 3.00 Å R-free 0.254
4ARR Crystal structure of the N-terminal domain of Drosophila Toll receptor with the magic triangle I3C Deposited 2012-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–228（201 aa） Fragment：TOLL RECEPTOR (UNP RESIDUES 28-228), VARIABLE LYMPHOCYTE RECEPTOR B.61 (UNP RESIDUES 133-201)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；SODIUM MALONATE AND 5-AMINO-2,4, 6-TRIIODOISOPHTHALIC ACID, pH 7
Resolution 3.00 Å R-free 0.254
4BV4 Structure and allostery in Toll-Spatzle recognition Deposited 2013-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 28–397（370 aa） Fragment：PROTEIN TOLL, RESIDUES 28-397, VARIABLE LYMPHOCYTE RECEPTOR B, RESIDUES 133-201
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；15% PEG 8000, 0.1M TRIS PH 7.5, 0.1 M MGCL2
Resolution 2.35 Å R-free 0.227
4LXS Structure of the Toll - Spatzle complex, a molecular hub in Drosophila development and innate immunity (glycosylated form) Deposited 2013-07-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 28–802（775 aa） Fragment：UNP residues 28-802
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；100 mM HEPES, 5% (v/v) propan-2-ol, 10% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution 3.30 Å R-free 0.264

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

View Construct and Data Evidence
UniProt name TOLL_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–775； UniProt 28–802

Protein spaetzle C-106

Drosophila melanogaster

UniProt P48607

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 3 其他Polymer 4 PDB declaration: trimeric（3） Consistent with protein copy count Chain J； UniProt 221–326 Chain K； UniProt 221–326 Not recorded Protein toll × 1 （P08953） ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；10% PEG 3350, 50 mM HEPES-Na salt, pH 7.5, vapor diffusion, hanging drop, temperature 287K Resolution 2.20 Å R-free 0.218

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 4LXR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3E07 Crystal structure of spatzle cystine knot Deposited 2008-07-31 Different construct 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 221–326（106 aa） Fragment：Spatzle cystine knot, Protein spaetzle C-106
Chain B 221–326（106 aa） Fragment：Spatzle cystine knot, Protein spaetzle C-106
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；50mM TRIS/HCl, 20% PEG 3350, 10mM betaine monohydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.265
4BV4 Structure and allostery in Toll-Spatzle recognition Deposited 2013-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 221–326（106 aa）
Chain M 221–326（106 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；15% PEG 8000, 0.1M TRIS PH 7.5, 0.1 M MGCL2
Resolution 2.35 Å R-free 0.227
4LXS Structure of the Toll - Spatzle complex, a molecular hub in Drosophila development and innate immunity (glycosylated form) Deposited 2013-07-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 221–326（106 aa）
Chain K 221–326（106 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；100 mM HEPES, 5% (v/v) propan-2-ol, 10% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution 3.30 Å R-free 0.264

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

View Construct and Data Evidence
UniProt name SPZ_DROME
Isoform —
PDB entities 2
Chains and sequence ranges Author chain J； PDBConstruct 1–106； UniProt 221–326 Author chain K； PDBConstruct 1–106； UniProt 221–326

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 4lxr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4lxr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4lxr
Deposition date deposition_date2013-07-30
Structure title titleStructure of the Toll - Spatzle complex, a molecular hub in Drosophila development and innate immunity
Keywords keywords;TLR, LEUCINE-RICH REPEAT, IMMUNE SYSTEM, CYTOKINE RECEPTOR, EMBRYONIC DEVELOPMENT, INNATE IMMUNITY, RECEPTOR-LIGAND COMPLEX', IMMUNE SYSTEM-CYTOKINE complex ;; IMMUNE SYSTEM/CYTOKINE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.17 Å
Radius of gyration Rg (electron density) rg_electron42.68 Å
Forward intensity I(0) i0173596000.00
Molecular weight molecular_weight104510.0 kDa
Excluded volume excluded_volume129900 ų
Envelope volume envelope_volume182690 ų
Hydration-shell volume shell_volume38728 ų
Envelope diameter envelope_diameter149.1 Å
Shell Rg shell_rg43.12 Å
Envelope Rg envelope_rg42.72 Å
Shape Rg shape_rg42.65 Å
Total Rg total_rg42.81 Å
Total atoms total_atoms7314
Residues n_residues885
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax150.6 Å
Rg (real space) rg_real42.75 Å
Rg uncertainty (real space) rg_real_error2.31 Å
I(0) (real space) i0_real1.7360e+08
I(0) uncertainty (real space) i0_real_error3.5330e+06
Rg (reciprocal space) rg_reciprocal42.18 Å
I(0) (reciprocal space) i0_reciprocal173500000.0000
Solution quality estimate total_estimate0.7426
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.6 Å
Skewness Skewness skewness0.591
Kurtosis Kurtosis kurtosis-0.471
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20710000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.493; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.419; Smooth: 0.753
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4lxrA02
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4lxrJ00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
Domain ID domain_id4lxrK00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
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8. Citations (1)

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9. Files and Curves (10)