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- PDB-9qw2: Crystal structure of human lung surfactant protein D trimeric fra... -

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Basic information

Entry
Database: PDB / ID: 9qw2
TitleCrystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepII-HepI-PhosI ligand
ComponentsPulmonary surfactant-associated protein D
KeywordsSURFACTANT PROTEIN / Trimeric recombinant collectin fragment / neck+CRD / alpha-helical coiled-coil / carbohydrate recognition domain / lectin / sugar binding protein
Function / homology
Function and homology information


Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis ...Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis / Signal regulatory protein family interactions / negative regulation of interleukin-2 production / lung alveolus development / macrophage chemotaxis / endocytic vesicle / negative regulation of T cell proliferation / multivesicular body / regulation of cytokine production / reactive oxygen species metabolic process / receptor-mediated endocytosis / positive regulation of phagocytosis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / SARS-CoV-1 activates/modulates innate immune responses / carbohydrate binding / lysosome / defense response to bacterium / innate immune response / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / 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. ...Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / 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
Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsShrive, A.K. / Greenhough, T.J. / Williams, H.M.
Funding support United Kingdom, Ireland, 4items
OrganizationGrant numberCountry
Diamond Light SourceMX14692 United Kingdom
Diamond Light SourceMX19880 United Kingdom
Science Foundation Ireland08/IN.1/B2067 Ireland
Science Foundation Ireland13/IA/1959 Ireland
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Phosphorylation of inner core heptose is a major determinant of bacterial surface lipopolysaccharide recognition by the innate immune protein hSP-D.
Authors: Williams, H.M. / Watson, A. / Madsen, J. / Clark, H.W. / Hood, D.W. / Oscarson, S. / Greenhough, T.J. / Shrive, A.K.
History
DepositionApr 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pulmonary surfactant-associated protein D
B: Pulmonary surfactant-associated protein D
C: Pulmonary surfactant-associated protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,83014
Polymers56,5053
Non-polymers1,32511
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Trimer previously established in literature using a range of methods including gel filtration, EM, crystal structure, homology etc
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-146 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.439, 108.179, 55.650
Angle α, β, γ (deg.)90.000, 90.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pulmonary surfactant-associated protein D / SP-D / Collectin-7 / Lung surfactant protein D


Mass: 18834.957 Da / Num. of mol.: 3 / Fragment: Trimeric neck + carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Details: C-terminal fragment aa 179-355 / Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, COLEC7, PSPD, SFTP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35247
#2: Polysaccharide L-glycero-alpha-D-manno-heptopyranose-(1-3)-4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose


Type: oligosaccharide / Mass: 482.329 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a11221h-1a_1-5_4*OPO/3O/3=O][a11221h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(4+0)][P]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 16% PEG 4000 and 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.92→55.64 Å / Num. obs: 49393 / % possible obs: 98.8 % / Redundancy: 2.6 % / CC1/2: 0.973 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 3 / Num. unique obs: 3267 / CC1/2: 0.788 / % possible all: 98

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→55.493 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.83 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2119 2478 5.02 %
Rwork0.1805 46887 -
all0.182 --
obs-49365 98.712 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.081 Å2-0 Å2-0.018 Å2
2--0.655 Å2-0 Å2
3----0.736 Å2
Refinement stepCycle: LAST / Resolution: 1.92→55.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 71 335 3760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163200
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6644735
X-RAY DIFFRACTIONr_angle_other_deg1.3661.67401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9625436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27625.398176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5915565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.308159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
X-RAY DIFFRACTIONr_nbd_refined0.2220.2743
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.22776
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21753
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21549
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2268
X-RAY DIFFRACTIONr_metal_ion_refined0.1140.233
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1310.210
X-RAY DIFFRACTIONr_nbd_other0.20.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.213
X-RAY DIFFRACTIONr_mcbond_it1.8712.0711753
X-RAY DIFFRACTIONr_mcbond_other1.8662.071752
X-RAY DIFFRACTIONr_mcangle_it2.8713.0912186
X-RAY DIFFRACTIONr_mcangle_other2.8723.0922187
X-RAY DIFFRACTIONr_scbond_it2.9692.4681746
X-RAY DIFFRACTIONr_scbond_other2.9532.4631742
X-RAY DIFFRACTIONr_scangle_it4.6613.5532549
X-RAY DIFFRACTIONr_scangle_other4.6633.5462544
X-RAY DIFFRACTIONr_lrange_it6.00925.984042
X-RAY DIFFRACTIONr_lrange_other5.91225.5623962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.2111820.2223402X-RAY DIFFRACTION98.0306
1.97-2.0240.2532080.2073368X-RAY DIFFRACTION99.3333
2.024-2.0820.2271810.1963292X-RAY DIFFRACTION99.2286
2.082-2.1470.2092160.1883135X-RAY DIFFRACTION98.7331
2.147-2.2170.2291440.1873133X-RAY DIFFRACTION99.1228
2.217-2.2950.1971420.1663011X-RAY DIFFRACTION99.2446
2.295-2.3810.2091100.1652922X-RAY DIFFRACTION98.9233
2.381-2.4780.2271390.1672778X-RAY DIFFRACTION98.9149
2.478-2.5890.2041240.1762677X-RAY DIFFRACTION98.592
2.589-2.7150.2291450.1822544X-RAY DIFFRACTION98.5704
2.715-2.8620.2331380.1772397X-RAY DIFFRACTION98.6381
2.862-3.0350.2131490.1742276X-RAY DIFFRACTION98.6574
3.035-3.2440.2071120.1782180X-RAY DIFFRACTION99.0921
3.244-3.5040.2061350.1791950X-RAY DIFFRACTION97.8414
3.504-3.8380.186730.1671875X-RAY DIFFRACTION98.9837
3.838-4.2910.187810.1631688X-RAY DIFFRACTION97.5193
4.291-4.9530.171660.1661471X-RAY DIFFRACTION98.1481
4.953-6.0630.203550.1981272X-RAY DIFFRACTION98.2963
6.063-8.5610.277500.219964X-RAY DIFFRACTION98.8304
8.561-55.4930.195280.197552X-RAY DIFFRACTION97.1524

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