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- PDB-4arr: Crystal structure of the N-terminal domain of Drosophila Toll rec... -

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Basic information

Entry
Database: PDB / ID: 4arr
TitleCrystal structure of the N-terminal domain of Drosophila Toll receptor with the magic triangle I3C
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


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' ...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 / TIR domain binding / 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 / virion binding / cytokine receptor activity / 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 / external side of plasma membrane / innate immune response / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / 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) / Toll-like receptor / 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) / Toll-like receptor / 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 / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / 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 / Alpha Beta
Similarity search - Domain/homology
Chem-I3C / Protein toll / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
EPTATRETUS BURGERI (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsGangloff, M. / Gay, N.J.
CitationJournal: 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 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6977
Polymers63,9162
Non-polymers1,7815
Water00
1
A: TOLL RECEPTOR, VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9594
Polymers31,9581
Non-polymers1,0013
Water0
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)32,7383
Polymers31,9581
Non-polymers7802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.643, 87.643, 220.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 31957.838 Da / Num. of mol.: 2
Fragment: TOLL RECEPTOR (UNP RESIDUES 28-228), VARIABLE LYMPHOCYTE RECEPTOR B.61 (UNP RESIDUES 133-201)
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
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#3: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H4I3NO4
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: 3.43 Å3/Da / Density % sol: 63.86 % / Description: NONE
Crystal growpH: 7
Details: SODIUM MALONATE AND 5-AMINO-2,4, 6-TRIIODOISOPHTHALIC ACID, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.7712
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 3→47.4 Å / Num. obs: 31669 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 13 % / Biso Wilson estimate: 79.11 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 12 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3→46.7 Å / Cor.coef. Fo:Fc: 0.8909 / Cor.coef. Fo:Fc free: 0.8391 / SU R Cruickshank DPI: 2.408 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.375 / SU Rfree Cruickshank DPI: 0.375
Details: RESIDUES 300-304 ARE DISORDERED. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 918 5.1 %RANDOM
Rwork0.2242 ---
obs0.2257 17997 99.9 %-
Displacement parametersBiso mean: 64.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.649 Å20 Å20 Å2
2---4.649 Å20 Å2
3---9.2979 Å2
Refine analyzeLuzzati coordinate error obs: 0.467 Å
Refinement stepCycle: LAST / Resolution: 3→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 74 0 4414
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074513HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.936114HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2157SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes114HARMONIC2
X-RAY DIFFRACTIONt_gen_planes667HARMONIC5
X-RAY DIFFRACTIONt_it4513HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion3.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion607SEMIHARMONIC5
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_contact4999SEMIHARMONIC4
LS refinement shellResolution: 3→3.18 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2802 166 5.86 %
Rwork0.254 2666 -
all0.2556 2832 -
obs--99.9 %
Refinement TLS params.

T33: -0.304 Å2 / 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)Origin x (Å)Origin y (Å)Origin z (Å)
14.9744-0.86950.05170.73640.14781.1905-0.04090.21760.01990.0020.016-0.0402-0.1176-0.16490.0249-0.1729-0.06920.0197-0.22320.027-36.723-4.86014.8004
21.469-1.88890.14474.5826-0.70380.926-0.00980.1601-0.03290.0413-0.1223-0.0506-0.19290.16620.1321-0.2527-0.0341-0.0085-0.14930.0096-44.3195-10.652230.6402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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