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- PDB-6bbe: Structure of N-glycosylated porcine surfactant protein-D -

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Basic information

Entry
Database: PDB / ID: 6bbe
TitleStructure of N-glycosylated porcine surfactant protein-D
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 / 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
Chem-1PG / Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / 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 / Category: citation / citation_author
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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 24, 2021Group: Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity_src_gen / struct_conn
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_conn.pdbx_leaving_atom_flag

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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)18,6945
Polymers17,0441
Non-polymers1,6504
Water1,20767
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)56,08115
Polymers51,1323
Non-polymers4,94912
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 area12530 Å2
ΔGint-14 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.015, 66.015, 64.658
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 17043.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SFTPD / 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-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 1317.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3-1/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(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-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion
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: Jun 20, 2013
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: 12220 / % possible obs: 96 % / Redundancy: 6.5 % / Biso Wilson estimate: 34.17 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.64 / Net I/σ(I): 25.4 / Num. measured all: 79516
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.974.50.37610451.729182.2
1.97-2.055.80.31512401.777199
2.05-2.146.80.28812691.8241100
2.14-2.2570.22312611.814199.8
2.25-2.3970.16512731.7261100
2.39-2.587.10.12612681.5671100
2.58-2.837.10.09212711.596199.9
2.83-3.246.90.06712411.584198
3.24-4.076.40.04512061.475193.6
4.071-156.10.03711461.289187.4

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHENIXphasing
RefinementResolution: 1.898→14.699 Å / FOM work R set: 0.7634 / SU ML: 0.27 / σ(F): 0 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2501 1184 10.17 %
Rwork0.2232 10453 -
obs0.2259 11637 91.51 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.237 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 150.73 Å2 / Biso mean: 47.45 Å2 / Biso min: 28.13 Å2
Baniso -1Baniso -2Baniso -3
1-9.4814 Å2-0 Å2-0 Å2
2--9.4814 Å2-0 Å2
3----18.9627 Å2
Refinement stepCycle: final / Resolution: 1.898→14.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 108 67 1368
Biso mean--66.5 50.01 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131367
X-RAY DIFFRACTIONf_angle_d0.8051867
X-RAY DIFFRACTIONf_chiral_restr0.051210
X-RAY DIFFRACTIONf_plane_restr0.005232
X-RAY DIFFRACTIONf_dihedral_angle_d26.386546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8979-1.98410.37761340.3106104475
1.9841-2.08840.28911420.243130992
2.0884-2.21880.26221460.231134695
2.2188-2.38950.25011520.238136896
2.3895-2.62870.28471560.2273135295
2.6287-3.00630.28171570.2269139097
3.0063-3.77690.24041550.2275136396
3.7769-150.21761420.2044128188

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