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- PDB-8suf: The complex of TOL-1 ectodomain bound to LAT-1 Lectin domain -

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Basic information

Entry
Database: PDB / ID: 8suf
TitleThe complex of TOL-1 ectodomain bound to LAT-1 Lectin domain
Components
  • Latrophilin-like protein 1
  • TIR domain-containing protein
KeywordsCELL ADHESION / Cell Surface Receptor
Function / homology
Function and homology information


cell development / sexual reproduction / self proteolysis / embryo development ending in birth or egg hatching / anterior/posterior pattern specification / extracellular matrix / defense response / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity ...cell development / sexual reproduction / self proteolysis / embryo development ending in birth or egg hatching / anterior/posterior pattern specification / extracellular matrix / defense response / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity / carbohydrate binding / defense response to Gram-negative bacterium / endopeptidase activity / cell surface receptor signaling pathway / extracellular space / membrane / plasma membrane
Similarity search - Function
: / : / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile. / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif ...: / : / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile. / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / TIR domain / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / 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
Similarity search - Domain/homology
Latrophilin-like protein 1 / TIR domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsCarmona Rosas, G. / Li, J. / Arac, D. / Ozkan, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM148412 United States
CitationJournal: To Be Published
Title: Structural basis and functional roles for Toll-like receptor binding to Latrophilin adhesion-GPCR in embryo development
Authors: Carmona Rosas, G. / Li, J. / Smith, J.S. / Cheng, S. / Baltrusaitis, E. / Nawrocka, W.I. / Zhao, M. / Kratsios, P. / Arac, D. / Ozkan, E.
History
DepositionMay 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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: TIR domain-containing protein
B: TIR domain-containing protein
C: TIR domain-containing protein
D: TIR domain-containing protein
E: Latrophilin-like protein 1
F: Latrophilin-like protein 1
G: Latrophilin-like protein 1
H: Latrophilin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,33728
Polymers499,2608
Non-polymers8,07720
Water00
1
A: TIR domain-containing protein
E: Latrophilin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0768
Polymers124,8152
Non-polymers2,2616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TIR domain-containing protein
F: Latrophilin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,4008
Polymers124,8152
Non-polymers2,5856
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TIR domain-containing protein
G: Latrophilin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5936
Polymers124,8152
Non-polymers1,7784
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TIR domain-containing protein
H: Latrophilin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,2686
Polymers124,8152
Non-polymers1,4534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.152, 316.755, 172.441
Angle α, β, γ (deg.)90.000, 90.160, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 27 through 695 or resid 700 through 983 or resid 2011 through 2021))
d_2ens_1(chain "B" and (resid 27 through 983 or resid 2011 through 2012))
d_3ens_1(chain "C" and (resid 27 through 695 or resid 700 through 983 or resid 2011 through 2051))
d_4ens_1(chain "D" and (resid 27 through 695 or resid 700 through 983 or resid 2011 through 2012))
d_1ens_2(chain "E" and resid 29 through 133)
d_2ens_2(chain "F" and resid 29 through 133)
d_3ens_2(chain "G" and resid 29 through 133)
d_4ens_2chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUASPASPAA27 - 69534 - 702
d_12ens_1TYRTYRPROPROAA700 - 983707 - 990
d_13ens_1NAGNAGNAGNAGAS1101
d_14ens_1NAGNAGNAGNAGII1
d_21ens_1GLUGLUPROPROBB27 - 98334 - 990
d_22ens_1NAGNAGNAGNAGLL1
d_23ens_1NAGNAGNAGNAGLL2
d_31ens_1GLUGLUASPASPCC27 - 69534 - 702
d_32ens_1TYRTYRPROPROCC700 - 983707 - 990
d_33ens_1NAGNAGNAGNAGCY1101
d_34ens_1NAGNAGNAGNAGOO1
d_41ens_1GLUGLUASPASPDD27 - 69534 - 702
d_42ens_1TYRTYRPROPRODD700 - 983707 - 990
d_43ens_1NAGNAGNAGNAGQQ1
d_44ens_1NAGNAGNAGNAGQQ2
d_11ens_2ALAALACYSCYSEE29 - 1331 - 105
d_21ens_2ALAALACYSCYSFF29 - 1331 - 105
d_31ens_2ALAALACYSCYSGG29 - 1331 - 105
d_41ens_2ALAALACYSCYSHH29 - 1331 - 105

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.991581021888, -0.108698702074, -0.070368097874), (0.0937964797422, 0.977602974934, -0.188400222365), (0.0892709214637, 0.18021380515, 0.979568112494)6.76331798568, -25.8179928654, 77.0929598037
2given(0.997217536701, 0.0502163798141, -0.0550953690801), (0.048660395391, -0.998387600554, -0.0292295223955), (-0.056474334136, 0.0264672298786, -0.998053172595)-42.7732900247, -70.3529746457, -215.32723102
3given(0.98953847067, -0.14029034673, -0.0336486801966), (-0.132337624748, -0.975541394619, 0.175515641639), (-0.0574488306282, -0.169226493193, -0.983901430968)-26.3521670021, -40.6888892904, -121.720994022
4given(0.999496217222, 0.006520727343, 0.0310610990508), (-0.00771317070308, 0.999231662362, 0.0384264483304), (-0.030786665247, -0.0386466693067, 0.998778562142)12.0117911248, 4.8140900998, 93.8123259241
5given(0.98897947898, -0.0454680643682, -0.140897996011), (-0.0554116305268, -0.996181316225, -0.0674710041899), (-0.137292175158, 0.0745348262669, -0.987722338673)-49.1824492667, -69.3506008928, -211.440484054
6given(0.553821096507, -0.80559741031, 0.210463786827), (-0.789753355633, -0.588312795886, -0.173717274511), (0.263764725333, -0.0700061904339, -0.962043295788)73.2716480206, -48.5753259301, -141.102728397

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
TIR domain-containing protein


Mass: 112253.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Construct is secreted by a signal peptide, cleaved and not present in mature protein, and has N-terminal His and Avi tags.
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tol-1, C07F11.1, CELE_C07F11.1 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9N5Z3
#2: Protein
Latrophilin-like protein 1


Mass: 12561.144 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Construct is secreted by a signal peptide, cleaved and not present in mature protein, and has a C-terminal His-tag. Contains isoform a for LAT-1 protein.
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lat-1, B0457.1 / Variant: isoform a / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G5EDW2

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Sugars , 6 types, 20 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-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: 748.682 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-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: 910.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#8: 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.: 10 / Source method: obtained synthetically / 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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Details

Has ligand of interestN
Has protein modificationY

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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: 4.37 Å3/Da / Density % sol: 71.86 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Sodium Malonate, 0.1 M Bis-Tris Propane pH 7.5, 26% PEG 3350, 1.2% Myo-Inositol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4→200 Å / Num. obs: 37159 / % possible obs: 55.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 139.85 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 6.2
Reflection shellResolution: 4→4.42 Å / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2858 / CC1/2: 0.603 / Rsym value: 0.727 / % possible all: 16.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→74.15 Å / SU ML: 0.8107 / Cross valid method: FREE R-VALUE / Phase error: 48.2417
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3377 1858 5.01 %
Rwork0.2883 35233 -
obs0.2908 37091 55.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 197.65 Å2
Refinement stepCycle: LAST / Resolution: 4→74.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32463 0 530 0 32993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006533537
X-RAY DIFFRACTIONf_angle_d1.080745503
X-RAY DIFFRACTIONf_chiral_restr0.05855516
X-RAY DIFFRACTIONf_plane_restr0.00695830
X-RAY DIFFRACTIONf_dihedral_angle_d11.475212683
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS7.09361746616
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.64289511289
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS7.80906715893
ens_2d_2EEX-RAY DIFFRACTIONTorsion NCS0.44868721748
ens_2d_3EEX-RAY DIFFRACTIONTorsion NCS0.772750042714
ens_2d_4EEX-RAY DIFFRACTIONTorsion NCS0.727044050531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.110.4627240.3205477X-RAY DIFFRACTION9.69
4.11-4.230.403470.3333759X-RAY DIFFRACTION16.04
4.23-4.370.3695690.31091032X-RAY DIFFRACTION21.14
4.37-4.520.276650.28541437X-RAY DIFFRACTION29.85
4.52-4.710.35421090.271794X-RAY DIFFRACTION36.79
4.71-4.920.28821110.25372185X-RAY DIFFRACTION44.74
4.92-5.180.32991380.26572624X-RAY DIFFRACTION54.24
5.18-5.50.30011910.27883044X-RAY DIFFRACTION63.01
5.5-5.930.32521800.29243586X-RAY DIFFRACTION73.54
5.93-6.520.38181770.30034154X-RAY DIFFRACTION84.39
6.52-7.470.36772500.32094527X-RAY DIFFRACTION92.33
7.47-9.410.38362510.33234826X-RAY DIFFRACTION98.43
9.41-74.150.31112460.26214788X-RAY DIFFRACTION97.09

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