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

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Basic information

Entry
Database: PDB / ID: 9qvu
TitleCrystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepI-(1,5)-KdoI 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
L-glycero-alpha-D-manno-heptopyranose / Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 12, 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)57,28614
Polymers56,5053
Non-polymers78111
Water6,936385
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 area7370 Å2
ΔGint-151 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.181, 106.780, 55.469
Angle α, β, γ (deg.)90.000, 92.250, 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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-GMH / L-glycero-alpha-D-manno-heptopyranose / L-glycero-alpha-D-manno-heptose / L-glycero-D-manno-heptose / L-glycero-manno-heptose / L-GLYCERO-D-MANNO-HEPTOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 210.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LDmanHepSNFG CARBOHYDRATE SYMBOLGMML 1.0
L-gro-a-D-manHeppIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
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: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.75→55.43 Å / Num. obs: 63620 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.9
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3 / Num. unique obs: 3472 / CC1/2: 0.753 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→55.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.024 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.206 3268 5.136 %
Rwork0.174 60039 -
all0.171 --
obs-63620 98.1 %
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: 24.718 Å2
Baniso -1Baniso -2Baniso -3
1--0.071 Å2-0 Å2-0.001 Å2
2--0.68 Å20 Å2
3----0.607 Å2
Refinement stepCycle: LAST / Resolution: 1.75→55.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 37 385 3886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.2812110.244443X-RAY DIFFRACTION97.0999
1.795-1.8450.2672330.2264257X-RAY DIFFRACTION97.0391
1.845-1.8980.2432490.2164124X-RAY DIFFRACTION96.8979
1.898-1.9570.2212020.1954043X-RAY DIFFRACTION97.4966
1.957-2.0210.2112100.183965X-RAY DIFFRACTION97.6608
2.021-2.0920.1962290.1723717X-RAY DIFFRACTION96.6446
2.092-2.170.2032280.1633641X-RAY DIFFRACTION97.4314
2.17-2.2590.2032140.1693570X-RAY DIFFRACTION98.1837
2.259-2.3590.1681670.1563413X-RAY DIFFRACTION98.1629
2.359-2.4750.1851650.1463282X-RAY DIFFRACTION98.1772
2.475-2.6080.1851580.1523157X-RAY DIFFRACTION98.6901
2.608-2.7660.2091640.1632928X-RAY DIFFRACTION98.3148
2.766-2.9570.1841410.1532797X-RAY DIFFRACTION98.8227
2.957-3.1940.2061210.1632598X-RAY DIFFRACTION98.3363
3.194-3.4990.1871210.1712404X-RAY DIFFRACTION98.8645
3.499-3.9110.1931090.1592176X-RAY DIFFRACTION99.0035
3.911-4.5150.175900.1551927X-RAY DIFFRACTION98.9696
4.515-5.5270.234710.1641632X-RAY DIFFRACTION98.2689
5.527-7.8060.192740.2091256X-RAY DIFFRACTION99.1058
7.806-55.430.237320.166709X-RAY DIFFRACTION98.4064

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