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- PDB-4dn8: Structure of porcine surfactant protein D neck and carbohydrate r... -

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Basic information

Entry
Database: PDB / ID: 4dn8
TitleStructure of porcine surfactant protein D neck and carbohydrate recognition domain complexed with mannose
ComponentsPulmonary surfactant-associated protein D
KeywordsSUGAR BINDING PROTEIN / collectin / lectin / carbohydrate/sugar binding / lung surfactant
Function / homology
Function and homology information


Toll Like Receptor 4 (TLR4) Cascade / Signal regulatory protein family interactions / Regulation of TLR by endogenous ligand / Surfactant metabolism / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / extracellular matrix structural constituent conferring tensile strength / respiratory gaseous exchange by respiratory system / collagen trimer / surfactant homeostasis / lung alveolus development ...Toll Like Receptor 4 (TLR4) Cascade / Signal regulatory protein family interactions / Regulation of TLR by endogenous ligand / Surfactant metabolism / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / extracellular matrix structural constituent conferring tensile strength / respiratory gaseous exchange by respiratory system / collagen trimer / surfactant homeostasis / lung alveolus development / positive regulation of phagocytosis / multivesicular body / extracellular matrix organization / carbohydrate binding / collagen-containing extracellular matrix / innate immune response / extracellular space
Similarity search - Function
Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / 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. ...Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / 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
beta-D-mannopyranose / Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
Authorsvan Eijk, M. / Rynkiewicz, M.J. / White, M.R. / Hartshorn, K.L. / Zou, X. / Schulten, K. / Luo, D. / Crouch, E.C. / Cafarella, T.M. / Head, J.F. ...van Eijk, M. / Rynkiewicz, M.J. / White, M.R. / Hartshorn, K.L. / Zou, X. / Schulten, K. / Luo, D. / Crouch, E.C. / Cafarella, T.M. / Head, J.F. / Haagsman, H.P. / Seaton, B.A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: A Unique Sugar-binding Site Mediates the Distinct Anti-influenza Activity of Pig Surfactant Protein D.
Authors: van Eijk, M. / Rynkiewicz, M.J. / White, M.R. / Hartshorn, K.L. / Zou, X. / Schulten, K. / Luo, D. / Crouch, E.C. / Cafarella, T.R. / Head, J.F. / Haagsman, H.P. / Seaton, B.A.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Revision 1.3May 19, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3184
Polymers17,0581
Non-polymers2603
Water64936
1
A: Pulmonary surfactant-associated protein D
hetero molecules

A: Pulmonary surfactant-associated protein D
hetero molecules

A: Pulmonary surfactant-associated protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,95512
Polymers51,1743
Non-polymers7819
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7120 Å2
ΔGint-111 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.024, 66.024, 66.018
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 17057.996 Da / Num. of mol.: 1
Fragment: neck and carbohydrate recognition domain, UNP residues 223-378
Mutation: N303Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SFTPD / Plasmid: pUPE105.03 / Cell line (production host): HEK293 / Production host: Homo Sapiens (human) / References: UniProt: Q9N1X4
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12.3 mg/ml protein in 0.9 % sodium chloride, 5 mM EDTA, 15 mM calcium chloride, and 20 mM mannose was mixed with an equal volume of 0.1 M bistris (pH =6.5), 20% w/v PEG 3350, 200 mM magesium ...Details: 12.3 mg/ml protein in 0.9 % sodium chloride, 5 mM EDTA, 15 mM calcium chloride, and 20 mM mannose was mixed with an equal volume of 0.1 M bistris (pH =6.5), 20% w/v PEG 3350, 200 mM magesium chloride, and 15% v/v glycerol. Prior to data collection crystals were soaked in a 30% w/v D-mannose solution., VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 8327 / Num. obs: 8327 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 46.21 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 33.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 7.25 / Num. unique all: 839 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: A complex of pig SPD and glycerol solved by molecular replacement in the same space group using human SPD (pdb code 2GGU B chain)

2ggu


Resolution: 2.2→14.763 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 827 9.93 %RANDOM
Rwork0.1989 ---
all0.2028 8327 --
obs0.2028 8327 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.908 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4547 Å20 Å20 Å2
2---2.4547 Å20 Å2
3---4.9093 Å2
Refinement stepCycle: LAST / Resolution: 2.2→14.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 14 36 1244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021244
X-RAY DIFFRACTIONf_angle_d0.5421680
X-RAY DIFFRACTIONf_dihedral_angle_d12.737464
X-RAY DIFFRACTIONf_chiral_restr0.038180
X-RAY DIFFRACTIONf_plane_restr0.003226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.198-2.33520.32431360.26991217X-RAY DIFFRACTION97
2.3352-2.51460.30691330.23551243X-RAY DIFFRACTION100
2.5146-2.76620.28281410.23571247X-RAY DIFFRACTION100
2.7662-3.16310.27511370.21921263X-RAY DIFFRACTION100
3.1631-3.97220.2521390.19371257X-RAY DIFFRACTION100
3.9722-14.76350.18451410.17161273X-RAY DIFFRACTION100
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)
10.4109-0.16440.46690.57630.6880.8532-0.19460.26210.1379-0.17390.0337-0.1368-0.70910.61930.1230.4384-0.0112-0.03790.40480.03170.26-2.595942.812512.1843
26.869-2.82321.3163.2034-1.20581.8274-0.6978-0.52161.11240.42550.2142-1.0576-0.26720.12430.59590.37520.0492-0.22230.370.02620.573820.980440.097338.0508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 204:236)
2X-RAY DIFFRACTION2(chain A and resid 237:355)

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