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- PDB-3ikp: Crystal structure of inositol phosphate bound trimeric human lung... -

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Basic information

Entry
Database: PDB / ID: 3ikp
TitleCrystal structure of inositol phosphate bound trimeric human lung surfactant protein D
ComponentsPulmonary surfactant-associated protein D
KeywordsSUGAR BINDING PROTEIN / Trimeric recombinant fragment / neck+CRD / Collagen / Disulfide bond / Extracellular matrix / Gaseous exchange / Glycoprotein / Hydroxylation / Lectin / Secreted / Surface film
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 / positive regulation of phagocytosis / negative regulation of T cell proliferation / multivesicular body / receptor-mediated endocytosis / regulation of cytokine production / reactive oxygen species metabolic process / 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. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A ...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-MYO-INOSITOL-1-PHOSPHATE / Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous to native crystals / Resolution: 1.75 Å
AuthorsShrive, A.K. / Greenhough, T.J.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325
Authors: Shrive, A.K. / Martin, C. / Burns, I. / Paterson, J.M. / Martin, J.D. / Townsend, J.P. / Waters, P. / Clark, H.W. / Kishore, U. / Reid, K.B.M. / Greenhough, T.J.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: High-resolution structural insights into ligand binding and immune cell recognition by human lung surfactant protein D
Authors: Shrive, A.K. / Tharia, H.A. / Strong, P. / Kishore, U. / Burns, I. / Rizkallah, P.J. / Reid, K.B.M. / Greenhough, T.J.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_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_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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)57,42215
Polymers56,5053
Non-polymers91712
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-52 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.450, 107.720, 55.670
Angle α, β, γ (deg.)90.000, 91.230, 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: 18834.957 Da / Num. of mol.: 3 / Fragment: UNP residues 199-375 / Mutation: P180S
Source method: isolated from a genetically manipulated source
Details: trimeric fragment of human lung surfactant protein D comprising alpha helical neck and carbohydrate recognition domains
Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, PSPD, SFTP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35247
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IPD / D-MYO-INOSITOL-1-PHOSPHATE


Mass: 258.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Sep 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.75→55.9 Å / Num. all: 64923 / Num. obs: 64923 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 11.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9059 / Rsym value: 0.194

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.1.4data scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: isomorphous to native crystals
Starting model: 1pw9

1pw9


Resolution: 1.75→55.44 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3296 5 %random
Rwork0.198 ---
obs-64893 98.7 %-
Solvent computationBsol: 38.676 Å2
Displacement parametersBiso max: 57.84 Å2 / Biso mean: 24.484 Å2 / Biso min: 11.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.244 Å20 Å20.462 Å2
2---1.168 Å20 Å2
3---2.411 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→55.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 42 440 3946
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1951.5
X-RAY DIFFRACTIONc_scbond_it2.2862
X-RAY DIFFRACTIONc_mcangle_it1.7642
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
1.75-1.810.29713060.2797604292
1.81-1.890.27772950.2384646899
1.89-1.970.21513450.1978650499
1.97-2.070.19453320.19356523100
2.07-2.20.22093200.191660899.8
2.2-2.380.21413380.1897651599.9
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ipd_xplor_par.txt

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