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- PDB-8rcy: L-SIGN CRD in complex with Man84. -

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Basic information

Entry
Database: PDB / ID: 8rcy
TitleL-SIGN CRD in complex with Man84.
ComponentsC-type lectin domain family 4 member M
KeywordsSUGAR BINDING PROTEIN / L-SIGN / carbohydrate recognition domain / lectin / immune system / inhibitor.
Function / homology
Function and homology information


cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding ...cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding / receptor-mediated endocytosis of virus by host cell / viral genome replication / peptide antigen binding / calcium-dependent protein binding / signaling receptor activity / host cell / virus receptor activity / carbohydrate binding / adaptive immune response / receptor-mediated virion attachment to host cell / intracellular signal transduction / immune response / symbiont entry into host cell / external side of plasma membrane / innate immune response / virion attachment to host cell / extracellular region / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
: / C-type lectin domain family 4 member M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsThepaut, M. / Bouchikri, C. / Pollastri, S. / Bernardi, A. / Fieschi, F.
Funding support France, Italy, 3items
OrganizationGrant numberCountry
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)CBH-EUR-GS (ANR-17- EURE0003) France
Ministero dell Universita e della Ricerca Italy
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT) Italy
CitationJournal: Chem Sci / Year: 2024
Title: Unprecedented selectivity for homologous lectin targets: differential targeting of the viral receptors L-SIGN and DC-SIGN.
Authors: Delaunay, C. / Pollastri, S. / Thepaut, M. / Cavazzoli, G. / Belvisi, L. / Bouchikri, C. / Labiod, N. / Lasala, F. / Gimeno, A. / Franconetti, A. / Jimenez-Barbero, J. / Arda, A. / Delgado, ...Authors: Delaunay, C. / Pollastri, S. / Thepaut, M. / Cavazzoli, G. / Belvisi, L. / Bouchikri, C. / Labiod, N. / Lasala, F. / Gimeno, A. / Franconetti, A. / Jimenez-Barbero, J. / Arda, A. / Delgado, R. / Bernardi, A. / Fieschi, F.
History
DepositionDec 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-type lectin domain family 4 member M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2634
Polymers15,8231
Non-polymers4403
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.430, 48.890, 35.670
Angle α, β, γ (deg.)90.00, 103.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C-type lectin domain family 4 member M / CD209 antigen-like protein 1 / DC-SIGN-related protein / DC-SIGNR / Dendritic cell-specific ICAM-3- ...CD209 antigen-like protein 1 / DC-SIGN-related protein / DC-SIGNR / Dendritic cell-specific ICAM-3-grabbing non-integrin 2 / DC-SIGN2 / Liver/lymph node-specific ICAM-3-grabbing non-integrin / L-SIGN


Mass: 15823.151 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CSO at position 133 of the sequence is the result of a Cys oxidation after production of the original sequence (i.e. Cys was into the original clone).
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4M, CD209L, CD209L1, CD299 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2X3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-A1H0Q / 1-[[1-[(2S,3S,4R,5S,6R)-2-(2-chloroethyloxy)-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methyl]guanidine


Mass: 364.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21ClN6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.79 Å3/Da / Density % sol: 31.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystallization technique: sitting drop of 150 nL (ratio 2:1, protein:precipitant). Protein stock: 20 mg / mL into 150 mM NaCl, 25 mM TRIS 8, 4 mM CaCl2. 200 nL Precipitant: PEG Suite Qiagen ...Details: Crystallization technique: sitting drop of 150 nL (ratio 2:1, protein:precipitant). Protein stock: 20 mg / mL into 150 mM NaCl, 25 mM TRIS 8, 4 mM CaCl2. 200 nL Precipitant: PEG Suite Qiagen H12 (0.18 M tri-Ammonium citrate, 20 %(w/v) PEG 3350).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.8→48.88 Å / Num. obs: 10206 / % possible obs: 97.5 % / Redundancy: 3.15 % / CC1/2: 0.996 / Net I/σ(I): 9.25
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 639 / CC1/2: 0.624

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.68 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.078 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 511 5 %RANDOM
Rwork0.16257 ---
obs0.16529 9695 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.935 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å21.67 Å2
2---1.52 Å2-0 Å2
3---0.93 Å2
Refinement stepCycle: 1 / Resolution: 1.8→34.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 26 138 1264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121233
X-RAY DIFFRACTIONr_bond_other_d0.0020.0151038
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.6441691
X-RAY DIFFRACTIONr_angle_other_deg1.431.5932397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2315151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47522.84188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69515190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.651510
X-RAY DIFFRACTIONr_chiral_restr0.5010.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021505
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02355
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9012.65560
X-RAY DIFFRACTIONr_mcbond_other1.8972.646559
X-RAY DIFFRACTIONr_mcangle_it2.9173.967704
X-RAY DIFFRACTIONr_mcangle_other2.9193.971705
X-RAY DIFFRACTIONr_scbond_it2.2482.882673
X-RAY DIFFRACTIONr_scbond_other2.2472.882674
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3894.222978
X-RAY DIFFRACTIONr_long_range_B_refined5.72331.0511521
X-RAY DIFFRACTIONr_long_range_B_other5.6430.641494
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 30 -
Rwork0.315 564 -
obs--79.31 %

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