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- PDB-6bbd: Structure of N-glycosylated porcine surfactant protein-D complexe... -

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Basic information

Entry
Database: PDB / ID: 6bbd
TitleStructure of N-glycosylated porcine surfactant protein-D complexed with glycerol
ComponentsPulmonary surfactant-associated protein D
KeywordsSURFACTANT PROTEIN / innate immunity / surfactant / N-linked glycan / C-type lectin
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 / respiratory gaseous exchange by respiratory system / collagen trimer / surfactant homeostasis / lung alveolus development / positive regulation of phagocytosis ...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 / respiratory gaseous exchange by respiratory system / collagen trimer / surfactant homeostasis / lung alveolus development / positive regulation of phagocytosis / multivesicular body / carbohydrate binding / 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 ...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
Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.898 Å
Authorsvan Eijk, M. / Rynkiewicz, M.J. / Khatri, K. / Leymarie, N. / Zaia, J. / White, M.R. / Hartshorn, K.L. / Cafarella, T.R. / van Die, I. / Hessing, M. ...van Eijk, M. / Rynkiewicz, M.J. / Khatri, K. / Leymarie, N. / Zaia, J. / White, M.R. / Hartshorn, K.L. / Cafarella, T.R. / van Die, I. / Hessing, M. / Seaton, B.A. / Haagsman, H.P.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Open Technology Program Grant10388 Netherlands
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Lectin-mediated binding and sialoglycans of porcine surfactant protein D synergistically neutralize influenza A virus.
Authors: van Eijk, M. / Rynkiewicz, M.J. / Khatri, K. / Leymarie, N. / Zaia, J. / White, M.R. / Hartshorn, K.L. / Cafarella, T.R. / van Die, I. / Hessing, M. / Seaton, B.A. / Haagsman, H.P.
History
DepositionOct 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,9985
Polymers16,8741
Non-polymers1,1244
Water1,24369
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)53,99415
Polymers50,6213
Non-polymers3,37212
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 area10070 Å2
ΔGint-75 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.798, 66.798, 64.974
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-228-

TYR

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Components

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


Mass: 16873.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SFTPD / Plasmid: pUPE105.03 / Cell line (production host): HEK293E / Production host: Homo sapiens (human) / References: UniProt: Q9N1X4
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 951.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1/a4-b1_b4-c1_c6-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystallized in hanging drops by mixing 5 ul protein with 5 ul reservoir solution (0.1 M 2-[bis(2-hydroxyethyl)-amino]-2-(hydroxymethyl)propane-1,3-diol, pH 6.5, 0.2 M MgCl2, 15% glycerol, and 22%-20% PEG 3350)

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 12304 / % possible obs: 94 % / Redundancy: 4.7 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.649 / Net I/σ(I): 23.2 / Num. measured all: 58032
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.972.80.3568711.358167.4
1.97-2.053.40.34111901.495192
2.05-2.144.30.32512961.654199.7
2.14-2.254.90.2913091.692199.7
2.25-2.3950.20213171.637199.8
2.39-2.585.10.1612891.64199.5
2.58-2.835.20.1212811.837198.3
2.83-3.245.10.08212841.799197.3
3.24-4.075.20.05312351.591194
4.07-155.40.03412321.516191.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4DN8

4dn8


Resolution: 1.898→14.852 Å / FOM work R set: 0.7832 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 1159 9.98 %
Rwork0.2008 10450 -
obs0.2053 11609 88.75 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.222 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 95.53 Å2 / Biso mean: 47.29 Å2 / Biso min: 24.69 Å2
Baniso -1Baniso -2Baniso -3
1-8.2546 Å2-0 Å2-0 Å2
2--8.2546 Å2-0 Å2
3----16.5092 Å2
Refinement stepCycle: final / Resolution: 1.898→14.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 72 69 1326
Biso mean--63.36 48.08 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141335
X-RAY DIFFRACTIONf_angle_d1.0851845
X-RAY DIFFRACTIONf_chiral_restr0.069199
X-RAY DIFFRACTIONf_plane_restr0.006233
X-RAY DIFFRACTIONf_dihedral_angle_d25.093514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8976-1.98380.3413970.289786996659
1.9838-2.08810.31061430.25121237138085
2.0881-2.21850.29191490.21791346149592
2.2185-2.38910.24581560.19521385154194
2.3891-2.62840.26021520.21271383153596
2.6284-3.0060.241590.21171434159397
3.006-3.77690.28561570.20311408156595
3.7769-14.85260.19641460.18181388153492
Refinement TLS params.

S33: 0.0001 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8344-0.8111-0.38070.79630.3730.17390.11190.3430.0051-0.1628-0.0775-0.01680.16450.39970.4254-0.0284-0.00390.4237-0.02010.347-2.689743.317312.5904
23.072-0.62660.58581.3279-0.77241.6134-0.1341-0.14540.08030.0519-0.0519-0.12330.03380.16280.26460.0022-0.02420.31840.0310.293720.941140.28338.0135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 205:235)A205 - 235
2X-RAY DIFFRACTION2chain 'A' and (resseq 236:358)A236 - 358

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