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- PDB-2ria: Crystal structure of the trimeric neck and carbohydrate recogniti... -

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Basic information

Entry
Database: PDB / ID: 2ria
TitleCrystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose
ComponentsPulmonary surfactant-associated protein D
KeywordsSUGAR BINDING PROTEIN / SURFACTANT PROTEIN / CARBOHYDRATE RECOGNITION / DOMAIN TRIMERIC
Function / homology
Function and homology information


Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / Regulation of TLR by endogenous ligand / respiratory gaseous exchange by respiratory system / Surfactant metabolism / collagen trimer ...Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / Regulation of TLR by endogenous ligand / respiratory gaseous exchange by respiratory system / 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 / positive regulation of phagocytosis / regulation of cytokine production / multivesicular body / reactive oxygen species metabolic process / extracellular matrix organization / receptor-mediated endocytosis / SARS-CoV-1 activates/modulates innate immune responses / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / collagen-containing extracellular matrix / 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. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain ...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. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
D-glycero-alpha-D-manno-heptopyranose / Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsWang, H. / Head, J. / Kosma, P. / Sheikh, S. / McDonald, B. / Smith, K. / Cafarella, T. / Seaton, B. / Crouch, E.
CitationJournal: Biochemistry / Year: 2008
Title: Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d.
Authors: Wang, H. / Head, J. / Kosma, P. / Brade, H. / Muller-Loennies, S. / Sheikh, S. / McDonald, B. / Smith, K. / Cafarella, T. / Seaton, B. / Crouch, E.
History
DepositionOct 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)52,80815
Polymers51,8173
Non-polymers99112
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.414, 108.606, 55.548
Angle α, β, γ (deg.)90.000, 91.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17272.209 Da / Num. of mol.: 3 / Fragment: neck and carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, PSPD, SFTP4 / Plasmid: PET30A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTABLUE / References: UniProt: P35247
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-289 / D-glycero-alpha-D-manno-heptopyranose


Type: D-saccharide, alpha linking / Mass: 210.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H14O7
IdentifierTypeProgram
D-gro-a-D-manHeppIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
DDmanHepSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 58216 / % possible obs: 95.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.069 / Χ2: 1.164 / Net I/σ(I): 23.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.842.40.33237741.03192.6
1.84-1.892.40.26138061.02795.6
1.89-1.942.50.20239031.00896
1.94-22.50.16438881.04295.7
2-2.062.50.13438701.05295.9
2.06-2.132.60.11239421.11596.7
2.13-2.222.50.09739271.05997.2
2.22-2.322.60.08839321.1597.6
2.32-2.442.60.07939401.17597.7
2.44-2.62.70.07439751.24697.6
2.6-2.82.80.06939681.18497.7
2.8-3.082.80.06338791.21596
3.08-3.522.90.06138691.33994.7
3.52-4.442.90.05938101.29893.7
4.44-5030.06337331.33989.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / FOM work R set: 0.856 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.237 5845 9.6 %
Rwork0.209 --
obs-57372 94.4 %
Solvent computationBsol: 50.289 Å2
Displacement parametersBiso mean: 26.903 Å2
Baniso -1Baniso -2Baniso -3
1-0.266 Å20 Å20.577 Å2
2---2.792 Å20 Å2
3---2.526 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 51 378 3774
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1447
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_mcbond_it1.2021.5
X-RAY DIFFRACTIONc_mcangle_it1.7732
X-RAY DIFFRACTIONc_scbond_it2.0132
X-RAY DIFFRACTIONc_scangle_it2.9492.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4ddh1.par

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