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- PDB-9emq: Crystal Structure of DC-SIGN in complex with AL86 -

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Basic information

Entry
Database: PDB / ID: 9emq
TitleCrystal Structure of DC-SIGN in complex with AL86
ComponentsDC-SIGN, CRD domain
KeywordsSUGAR BINDING PROTEIN / glyomimetic / DC-SIGN
Function / homology
Function and homology information


B cell adhesion / cell-cell recognition / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion / leukocyte cell-cell adhesion / pattern recognition receptor activity ...B cell adhesion / cell-cell recognition / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding / regulation of T cell proliferation / positive regulation of T cell proliferation / CD209 (DC-SIGN) signaling / viral genome replication / peptide antigen binding / endocytosis / host cell / virus receptor activity / carbohydrate binding / adaptive immune response / intracellular signal transduction / immune response / innate immune response / external side of plasma membrane / symbiont entry into host cell / virion attachment to host cell / cell surface / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJakob, R.P. / Cramer, J. / Maier, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)532758733 Germany
CitationJournal: J.Med.Chem. / Year: 2024
Title: Thermodynamics-Guided Design Reveals a Cooperative Hydrogen Bond in DC-SIGN-targeted Glycomimetics.
Authors: Nemli, D.D. / Jiang, X. / Jakob, R.P. / Gloder, L.M. / Schwardt, O. / Rabbani, S. / Maier, T. / Ernst, B. / Cramer, J.
History
DepositionMar 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DC-SIGN, CRD domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6855
Polymers18,1601
Non-polymers5254
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-25 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.290, 59.290, 74.295
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21A-730-

HOH

31A-739-

HOH

41A-742-

HOH

51A-751-

HOH

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Components

#1: Protein DC-SIGN, CRD domain / C-type lectin domain family 4 member L / Dendritic cell-specific ICAM-3-grabbing non-integrin 1 / ...C-type lectin domain family 4 member L / Dendritic cell-specific ICAM-3-grabbing non-integrin 1 / DC-SIGN / DC-SIGN1 / CD209 antigen


Mass: 18160.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD209, CLEC4L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NNX6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A1H5Z / (2~{R},3~{S},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-5-(4-phenyl-1,2,3-triazol-1-yl)-6-[[(3~{S})-piperidin-3-yl]methoxy]oxane-3,4-diol


Mass: 404.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15M KCl, 0.1M Hepes7.6, 14% PEG5000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 1.8→51.35 Å / Num. obs: 14473 / % possible obs: 99.8 % / Redundancy: 19.1 % / CC1/2: 0.971 / Rmerge(I) obs: 0.349 / Rpim(I) all: 0.08 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 18.8 % / Rmerge(I) obs: 1.511 / Mean I/σ(I) obs: 1 / Num. unique obs: 1428 / CC1/2: 0.63 / Rpim(I) all: 0.354 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→51.347 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 747 5.17 %
Rwork0.167 13703 -
obs0.1686 14450 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.58 Å2 / Biso mean: 23.6795 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: final / Resolution: 1.8→51.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 61 154 1285
Biso mean--29.91 33.27 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.9390.27021340.22782694
1.939-2.13420.18981550.17372687
2.1342-2.4430.18541370.16462719
2.443-3.07780.18791590.1682732
3.0778-51.3470.19611620.15392871
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)
13.18140.89820.23230.33260.7636.1807-0.10240.3010.1869-0.14640.0665-0.0373-0.08570.36490.03410.1707-0.01170.0230.20230.01870.1735-11.923431.4377-1.1972
22.0804-1.83461.22163.4194-1.66211.65210.02590.1201-0.0902-0.2485-0.0848-0.01140.13940.03180.07790.1365-0.01580.01270.1164-0.0030.2107-13.044625.45388.5619
31.670.0189-0.22910.8038-0.05620.85350.1167-0.06060.1660.0444-0.1427-0.3321-0.00060.10880.02780.1249-0.0062-0.00020.1580.00250.2137-6.930827.517215.6047
41.3156-0.5852-1.22286.7122.31463.0910.00910.0573-0.0521-0.2763-0.08180.37490.0432-0.1620.07550.1478-0.0116-0.00470.1568-0.00860.1537-22.773923.388612.6943
52.43311.09890.95092.57140.72210.9751-0.0074-0.1611-0.1278-0.0124-0.01-0.14090.0675-0.1365-0.02740.1662-0.0215-0.00970.16750.00520.1614-13.248419.338818.7705
60.372-0.44870.16230.9194-1.19012.68510.0844-0.66860.11410.4613-0.1907-0.238-0.43170.07120.14210.2671-0.1119-0.0580.3233-0.02940.1628-10.405127.18630.0206
71.58030.3021-0.29912.0309-0.20781.49340.1342-0.3859-0.01730.2534-0.1232-0.09490.0150.02010.01550.1635-0.0443-0.02690.2051-0.0070.1184-17.763521.312626.2158
83.0926-0.13910.60462.64430.50523.26790.0853-0.2706-0.28240.2005-0.1775-0.30460.22440.20.14890.1726-0.0132-0.01090.160.03990.3109-7.649915.758318.2862
92.5433-0.3532-0.15985.0508-2.98144.2861-0.03230.15280.3437-0.45150.0317-0.1108-0.27740.12660.04950.2002-0.0278-0.01230.12880.01530.2343-12.534834.52966.6388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 253 through 260 )A253 - 260
2X-RAY DIFFRACTION2chain 'A' and (resid 261 through 276 )A261 - 276
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 296 )A277 - 296
4X-RAY DIFFRACTION4chain 'A' and (resid 297 through 310 )A297 - 310
5X-RAY DIFFRACTION5chain 'A' and (resid 311 through 320 )A311 - 320
6X-RAY DIFFRACTION6chain 'A' and (resid 321 through 330 )A321 - 330
7X-RAY DIFFRACTION7chain 'A' and (resid 331 through 367 )A331 - 367
8X-RAY DIFFRACTION8chain 'A' and (resid 368 through 375 )A368 - 375
9X-RAY DIFFRACTION9chain 'A' and (resid 376 through 384 )A376 - 384

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