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- PDB-4bv4: Structure and allostery in Toll-Spatzle recognition -

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Entry
Database: PDB / ID: 4bv4
TitleStructure and allostery in Toll-Spatzle recognition
Components
  • PROTEIN SPAETZLE C-106
  • PROTEIN TOLL, VARIABLE LYMPHOCYTE RECEPTOR B CHIMERA
KeywordsIMMUNE SYSTEM / CYTOKINE RECOGNITION / EMBRYONIC DEVELOPMENT / INNATE IMMUNITY / LEUCINE-RICH REPEATS / CYSTINE-KNOT / GLYCOPROTEIN
Function / homology
Function and homology information


positive regulation of antimicrobial peptide biosynthetic process / positive regulation of antifungal peptide biosynthetic process / positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / defense response to oomycetes / 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 ...positive regulation of antimicrobial peptide biosynthetic process / positive regulation of antifungal peptide biosynthetic process / positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / defense response to oomycetes / 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 / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / Toll binding / central nervous system formation / TIR domain binding / oocyte dorsal/ventral axis specification / cell competition in a multicellular organism / larval somatic muscle development / positive regulation of antimicrobial peptide production / antifungal innate immune response / Neutrophil degranulation / dorsal/ventral axis specification / Toll signaling pathway / detection of virus / NAD+ nucleotidase, cyclic ADP-ribose generating / dorsal/ventral pattern formation / motor neuron axon guidance / virion binding / cytokine receptor activity / negative regulation of multicellular organism growth / cytokine binding / cleavage furrow / defense response to fungus / synapse assembly / negative regulation of insulin receptor signaling pathway / cytokine activity / growth factor activity / response to hydrogen peroxide / negative regulation of cell growth / response to wounding / transmembrane signaling receptor activity / signaling receptor activity / heart development / defense response to Gram-negative bacterium / killing of cells of another organism / negative regulation of neuron apoptotic process / receptor ligand activity / early endosome / cell adhesion / defense response to Gram-positive bacterium / external side of plasma membrane / innate immune response / positive regulation of gene expression / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spaetzle / Spaetzle / 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) / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain ...Spaetzle / Spaetzle / 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) / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Cystine-knot cytokine / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / 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 / Ribbon / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein toll / Protein spaetzle / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
EPTATRETUS BURGERI (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLewis, M.F. / Arnot, C.J. / Beeston, H. / McCoy, A. / Ashcroft, A.E. / Gay, N.J. / Gangloff, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Cytokine Spatzle Binds to the Drosophila Immunoreceptor Toll with a Neurotrophin-Like Specificity and Couples Receptor Activation.
Authors: Lewis, M. / Arnot, C.J. / Beeston, H. / Mccoy, A. / Ashcroft, A.E. / Gay, N.J. / Gangloff, M.
History
DepositionJun 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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.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.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 / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: PROTEIN SPAETZLE C-106
M: PROTEIN SPAETZLE C-106
R: PROTEIN TOLL, VARIABLE LYMPHOCYTE RECEPTOR B CHIMERA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0178
Polymers74,7353
Non-polymers2,2825
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint32.9 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.310, 57.110, 70.500
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN SPAETZLE C-106 / PROTEIN SPAETZLE


Mass: 11992.517 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PFASTBAC-1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P48607
#2: Protein PROTEIN TOLL, VARIABLE LYMPHOCYTE RECEPTOR B CHIMERA


Mass: 50749.930 Da / Num. of mol.: 1
Fragment: PROTEIN TOLL, RESIDUES 28-397, VARIABLE LYMPHOCYTE RECEPTOR B, RESIDUES 133-201
Source method: isolated from a genetically manipulated source
Details: CHIMERIC PROTEIN, GLYCAN BOUND
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
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpb1-6]DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-2-3-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: 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.: 4
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5 / Details: 15% PEG 8000, 0.1M TRIS PH 7.5, 0.1 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9788
DetectorDate: Sep 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.35→49.12 Å / Num. obs: 24588 / % possible obs: 74.8 % / Observed criterion σ(I): 2.6 / Redundancy: 3.9 % / Biso Wilson estimate: 52.36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.6 / % possible all: 32.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
ANISOSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ARN, 3E07

4arn

3e07


Resolution: 2.35→49.12 Å / Cor.coef. Fo:Fc: 0.9245 / Cor.coef. Fo:Fc free: 0.9032 / SU R Cruickshank DPI: 0.482 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.465 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.26
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 1256 5.11 %RANDOM
Rwork0.195 ---
obs0.1967 24588 74.74 %-
Displacement parametersBiso mean: 59.74 Å2
Baniso -1Baniso -2Baniso -3
1--6.3453 Å20 Å2-0.3304 Å2
2--12.2952 Å20 Å2
3----5.9499 Å2
Refine analyzeLuzzati coordinate error obs: 0.343 Å
Refinement stepCycle: LAST / Resolution: 2.35→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 150 104 4824
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094840HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.116576HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2305SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes130HARMONIC2
X-RAY DIFFRACTIONt_gen_planes678HARMONIC5
X-RAY DIFFRACTIONt_it4840HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion3.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion683SEMIHARMONIC5
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_contact5133SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.45 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2735 53 5.65 %
Rwork0.2122 885 -
all0.2159 938 -
obs--74.74 %
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)
12.1204-0.9804-2.43791.42441.59453.66940.0101-0.24780.17260.1074-0.040.1217-0.0465-0.00180.0298-0.2186-0.0690.00230.239-0.0665-0.1616400.3477-6.8524117.5984
22.3158-0.49510.0584.87082.79774.67630.008-0.12250.3149-0.01480.04330.0016-0.09920.0192-0.0513-0.2603-0.1111-0.02410.1725-0.0596-0.109410.9011-3.1092117.0293
32.7177-0.70930.58630.6657-0.18281.7993-0.0573-0.301-0.24740.1140.0820.020.16470.1882-0.0247-0.2718-0.04440.0273-0.0530.0398-0.2971410.6345-19.2876104.1815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN L
2X-RAY DIFFRACTION2CHAIN M
3X-RAY DIFFRACTION3CHAIN R

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