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- PDB-9srk: Structure of collectin-11 (CL-11) carbohydrate-recognition domain... -

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Basic information

Entry
Database: PDB / ID: 9srk
TitleStructure of collectin-11 (CL-11) carbohydrate-recognition domain in complex with L-fucose
ComponentsCollectin-11
KeywordsIMMUNE SYSTEM / Innate immunity / complement / lectin
Function / homology
Function and homology information


calcium-dependent carbohydrate binding / Lectin pathway of complement activation / positive regulation of opsonization / fucose binding / complement activation, lectin pathway / oligosaccharide binding / developmental process / cell surface pattern recognition receptor signaling pathway / collagen trimer / antimicrobial humoral response ...calcium-dependent carbohydrate binding / Lectin pathway of complement activation / positive regulation of opsonization / fucose binding / complement activation, lectin pathway / oligosaccharide binding / developmental process / cell surface pattern recognition receptor signaling pathway / collagen trimer / antimicrobial humoral response / serine-type endopeptidase complex / complement activation / Scavenging by Class A Receptors / execution phase of apoptosis / Initial triggering of complement / D-mannose binding / external side of plasma membrane / calcium ion binding / proteolysis / extracellular space / DNA binding / extracellular region / identical protein binding
Similarity search - Function
Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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) ...Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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
alpha-L-fucopyranose / beta-L-fucopyranose / Collectin-11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWallis, R. / Alrehaili, A.F.M. / Sacks, S.H. / klavinskis, L.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M012263/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Glycan recognition by collectin-11 drives SARS-CoV-2 infectivity and membrane injury of respiratory epithelial cells.
Authors: Polycarpou, A. / Wagner-Gamble, T. / Greenlaw, R. / O'Neill, L. / Kanabar, V. / Alrehaili, A. / Jeon, Y. / Baker, J. / Bafadhel, M. / Khan, H. / Malim, M.H. / Romano, M. / Farrar, C.A. / ...Authors: Polycarpou, A. / Wagner-Gamble, T. / Greenlaw, R. / O'Neill, L. / Kanabar, V. / Alrehaili, A. / Jeon, Y. / Baker, J. / Bafadhel, M. / Khan, H. / Malim, M.H. / Romano, M. / Farrar, C.A. / Smolarek, D. / Martinez-Nunez, R. / Doores, K.J. / Wallis, R. / Klavinskis, L.S. / Sacks, S.H.
History
DepositionSep 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 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: Collectin-11
B: Collectin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,24617
Polymers28,5702
Non-polymers1,67615
Water3,495194
1
A: Collectin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1849
Polymers14,2851
Non-polymers8998
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collectin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0628
Polymers14,2851
Non-polymers7777
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.090, 105.760, 45.320
Angle α, β, γ (deg.)90.000, 93.940, 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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Collectin-11 / Collectin kidney protein 1 / CL-K1


Mass: 14285.022 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COLEC11, UNQ596/PRO1182 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BWP8

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Sugars , 2 types, 8 molecules

#3: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 201 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-acetate pH 8.5 containing 25% PEG High Smear. Crystals were transferred to reservoir solution containing 15% (vol/vol) L-fucose (0.9 M), and incubated for 10 minutes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→52.81 Å / Num. obs: 27248 / % possible obs: 94.1 % / Redundancy: 1.6 % / Biso Wilson estimate: 19.64 Å2 / CC1/2: 1 / Net I/σ(I): 5.9
Reflection shellResolution: 1.7→1.74 Å / Num. unique obs: 1366 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.21 Å / SU ML: 0.1744 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1982 1203 5.02 %
Rwork0.1584 22757 -
obs0.1604 23960 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 102 194 2270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812126
X-RAY DIFFRACTIONf_angle_d0.95412873
X-RAY DIFFRACTIONf_chiral_restr0.0554318
X-RAY DIFFRACTIONf_plane_restr0.0066367
X-RAY DIFFRACTIONf_dihedral_angle_d12.4452800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.29721270.23932345X-RAY DIFFRACTION90.22
1.87-1.960.25581280.2072509X-RAY DIFFRACTION97.78
1.96-2.060.24481290.17942561X-RAY DIFFRACTION99.08
2.06-2.190.21371390.16332535X-RAY DIFFRACTION99.18
2.19-2.360.22981400.16742550X-RAY DIFFRACTION98.93
2.36-2.60.21551310.1642561X-RAY DIFFRACTION99.59
2.6-2.970.18341200.15712561X-RAY DIFFRACTION99.48
2.97-3.740.1851490.13952550X-RAY DIFFRACTION99.05
3.74-45.210.15921400.14142585X-RAY DIFFRACTION98.77
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)
12.20378268721-0.2648013604860.1259755741343.806868680311.188656878561.9922939142-0.00524071333949-0.05630305348480.142855096041-0.1870173712280.0197578952639-0.196570628885-0.01928724637050.1562121065630.00392296754690.1000258310630.01060120890340.03058788589760.15135881030.00973448007250.13411303204319.2568925765-7.2449038382541.481795075
21.85065140215-0.213876488817-0.111230690682.01001703628-1.249299465183.4497272819-0.102940238811-0.126305888473-0.1811179782450.2311596188830.02339002500380.1047839834090.181206406526-0.0005085144380910.05954321829250.157295087522-0.009607190797970.04810699973030.140868454480.01075439390430.15302848977511.827795818810.482621087818.3301157206
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 146 - 271 / Label seq-ID: 1 - 126

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 146 through 271)AA
22(chain 'B' and resid 146 through 271)BH

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