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- PDB-4arn: Crystal structure of the N-terminal domain of Drosophila Toll receptor -

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Basic information

Entry
Database: PDB / ID: 4arn
TitleCrystal structure of the N-terminal domain of Drosophila Toll receptor
ComponentsTOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
KeywordsIMMUNE SYSTEM / CYTOKINE RECEPTOR / EMBRYONIC DEVELOPMENT / INNATE IMMUNITY / LEUCINE-RICH REPEAT / LRR HYBRID TECHNOLOGY
Function / homology
Function and homology information


defense response to oomycetes / positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / synaptic target inhibition / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' ...defense response to oomycetes / positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / synaptic target inhibition / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' / positive regulation of antifungal peptide production / TIR domain binding / larval somatic muscle development / cell competition in a multicellular organism / positive regulation of antimicrobial peptide production / antifungal innate immune response / Neutrophil degranulation / dorsal/ventral axis specification / Toll signaling pathway / detection of virus / NAD+ nucleosidase activity, cyclic ADP-ribose generating / cytokine receptor activity / virion binding / negative regulation of multicellular organism growth / cytokine binding / cleavage furrow / synapse assembly / negative regulation of insulin receptor signaling pathway / negative regulation of cell growth / response to wounding / transmembrane signaling receptor activity / signaling receptor activity / heart development / early endosome / cell adhesion / defense response to Gram-positive bacterium / innate immune response / external side of plasma membrane / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane
Similarity search - Function
Leucine rich repeat C-terminal domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / BspA type Leucine rich repeat region / : / BspA type Leucine rich repeat region (6 copies) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain ...Leucine rich repeat C-terminal domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / BspA type Leucine rich repeat region / : / BspA type Leucine rich repeat region (6 copies) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / TIR domain profile. / Alpha-Beta Horseshoe / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Protein toll / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
EPTATRETUS BURGERI (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsGangloff, M. / Gay, N.J.
Citation
Journal: Structure / Year: 2013
Title: Functional Insights from the Crystal Structure of the N-Terminal Domain of the Prototypical Toll Receptor.
Authors: Gangloff, M. / Arnot, C.J. / Lewis, M. / Gay, N.J.
#1: Journal: J.Appl.Crystallogr. / Year: 2013
Title: Liesegang-Like Patterns of Toll Crystals Grown in Gel.
Authors: Gangloff, M. / Moreno, A. / Gay, N.J.
History
DepositionApr 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2May 8, 2013Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
B: TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
C: TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
D: TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,56115
Polymers127,8314
Non-polymers3,72911
Water5,819323
1
A: TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6484
Polymers31,9581
Non-polymers6913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7245
Polymers31,9581
Non-polymers7664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5853
Polymers31,9581
Non-polymers1,6282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6033
Polymers31,9581
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.787, 93.276, 225.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA / TOLL / VARIABLE LYMPHOCYTE RECEPTOR B


Mass: 31957.838 Da / Num. of mol.: 4
Fragment: TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201
Source method: isolated from a genetically manipulated source
Details: CHIMERIC PROTEIN
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly), (gene. exp.) EPTATRETUS BURGERI (inshore hagfish)
Plasmid: PFASTBAC-1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P08953, UniProt: Q4G1L2

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Sugars , 4 types, 9 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1203.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-3-2/a3-b1_a4-c1_a6-g1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 325 molecules

#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsVARIABLE LYMPHOCYTE RECEPTOR B.61 (GENBANK AAZ16361)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.59 % / Description: NONE
Crystal growpH: 7 / Details: PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→29.9 Å / Num. obs: 72977 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 61.38 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 2.41→2.54 Å / Redundancy: 6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.1 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHENIXAUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ARR

4arr


Resolution: 2.41→29.95 Å / Cor.coef. Fo:Fc: 0.9335 / Cor.coef. Fo:Fc free: 0.9281 / SU R Cruickshank DPI: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.185
Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 3668 5.04 %RANDOM
Rwork0.2009 ---
obs0.2017 72763 99.61 %-
Displacement parametersBiso mean: 66.68 Å2
Baniso -1Baniso -2Baniso -3
1--13.6731 Å20 Å20 Å2
2--2.3637 Å20 Å2
3---11.3093 Å2
Refine analyzeLuzzati coordinate error obs: 0.395 Å
Refinement stepCycle: LAST / Resolution: 2.41→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8688 0 245 323 9256
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089176HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9712449HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4415SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes226HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1312HARMONIC5
X-RAY DIFFRACTIONt_it9176HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion2.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1280SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9860SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2587 275 5.19 %
Rwork0.2391 5028 -
all0.2402 5303 -
obs--99.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75490.49090.16644.02480.23311.53210.0488-0.0391-0.0180.2077-0.05780.17010.4006-0.1610.0091-0.0195-0.00020.0205-0.17430.0188-0.219728.13477.621833.5971
23.70140.91590.58260.81090.5631.3145-0.24740.33630.2866-0.16970.25680.0867-0.32090.3412-0.0094-0.0596-0.0569-0.0103-0.08970.0279-0.203756.198941.023723.3205
32.4984-2.10540.32033.4456-0.25551.92070.08760.5053-0.0082-0.02-0.45490.07910.3851-0.06060.3673-0.2810.0127-0.00720.0667-0.0413-0.287821.108410.21954.3489
43.8681-0.76280.79461.67570.02741.77060.03590.06090.12170.1663-0.0770.15730.07930.29060.04110.14250.00570.0197-0.304-0.0189-0.268553.069246.356252.573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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