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- PDB-9g6w: L-SIGN CRD in complex with Man96. -

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Basic information

Entry
Database: PDB / ID: 9g6w
TitleL-SIGN CRD in complex with Man96.
ComponentsIsoform 1 of C-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 / innate immune response / external side of plasma membrane / symbiont entry into host cell / 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: 2 Å
AuthorsThepaut, M. / Cavazzoli, G. / Bernardi, A. / Fieschi, F.
Funding support France, Italy, 2items
OrganizationGrant numberCountry
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)CBH-EUR-GS (ANR-17- EURE0003) France
Ministero dell Universita e della RicercaPRIN 20224LLK82 Italy
CitationJournal: To be published
Title: L-SIGN CRD in complex with Man96.
Authors: Cavazzoli, G. / Pollastri, S. / Panzeri, A. / Sattin, S. / Belvisi, L. / Bernardi, A. / Delaunay, C. / Thepaut, M. / Fieschi, F.
History
DepositionJul 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 1 of C-type lectin domain family 4 member M
B: Isoform 1 of C-type lectin domain family 4 member M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,82913
Polymers31,6142
Non-polymers1,21511
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.720, 105.720, 59.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Isoform 1 of 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: 15807.151 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4M, CD209L, CD209L1, CD299 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2X3

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Non-polymers , 5 types, 163 molecules

#2: Chemical ChemComp-A1IIW / (2~{R},3~{S},4~{R},5~{S},6~{S})-6-(2-chloroethyloxy)-2-(hydroxymethyl)-5-[4-[(imidazolidin-2-ylideneamino)methyl]-1,2,3-triazol-1-yl]oxane-3,4-diol


Mass: 390.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H23ClN6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystallization technique: sitting drop of 100 nL of protein and 50 nL of precipitant). Protein stock: 20.1 mg/mL, 3.75 mM ligand into 150 mM NaCl, 25 mM TRIS 8, 4 mM CaCl2. Precipitant: 1- ...Details: Crystallization technique: sitting drop of 100 nL of protein and 50 nL of precipitant). Protein stock: 20.1 mg/mL, 3.75 mM ligand into 150 mM NaCl, 25 mM TRIS 8, 4 mM CaCl2. Precipitant: 1-13 of JCSG-plus screen Molecular Dimensions (0.8 M ammonium sulfate, 0.1 M citrate pH 4).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2→49.66 Å / Num. obs: 24815 / % possible obs: 96.9 % / Redundancy: 2.8 % / CC1/2: 0.99 / Net I/σ(I): 4.66
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1800 / CC1/2: 0.733 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.429 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28994 1241 5 %RANDOM
Rwork0.22751 ---
obs0.23059 23574 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.515 Å2
Baniso -1Baniso -2Baniso -3
1--2.96 Å2-1.48 Å2-0 Å2
2---2.96 Å20 Å2
3---9.59 Å2
Refinement stepCycle: 1 / Resolution: 2→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 68 152 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0112219
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161854
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.6453021
X-RAY DIFFRACTIONr_angle_other_deg0.5311.64268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8475254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.4776.66718
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50810324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
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_it3.6593.9041022
X-RAY DIFFRACTIONr_mcbond_other3.6593.9031022
X-RAY DIFFRACTIONr_mcangle_it5.3916.9811274
X-RAY DIFFRACTIONr_mcangle_other5.4056.9881275
X-RAY DIFFRACTIONr_scbond_it4.4564.2711197
X-RAY DIFFRACTIONr_scbond_other4.4554.2721198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6937.6271748
X-RAY DIFFRACTIONr_long_range_B_refined8.91442.842739
X-RAY DIFFRACTIONr_long_range_B_other8.8842.662720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 94 -
Rwork0.408 1787 -
obs--98.84 %

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