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- PDB-4m17: Crystal Structure of Surfactant Protein-D D325A/R343V mutant -

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Basic information

Entry
Database: PDB / ID: 4m17
TitleCrystal Structure of Surfactant Protein-D D325A/R343V mutant
ComponentsPulmonary surfactant-associated protein D
KeywordsSUGAR BINDING PROTEIN / surfactant protein / carbohydrate recognition domain / lectin
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 / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / 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 / 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 / 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
Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.096 Å
AuthorsGoh, B.C. / Rynkiewicz, M.J. / Cafarella, T.R. / White, M.R. / Hartshorn, K.L. / Allen, K. / Crouch, E.C. / Calin, O. / Seeberger, P.H. / Schulten, K. / Seaton, B.A.
CitationJournal: Biochemistry / Year: 2013
Title: Molecular mechanisms of inhibition of influenza by surfactant protein d revealed by large-scale molecular dynamics simulation.
Authors: Goh, B.C. / Rynkiewicz, M.J. / Cafarella, T.R. / White, M.R. / Hartshorn, K.L. / Allen, K. / Crouch, E.C. / Calin, O. / Seeberger, P.H. / Schulten, K. / Seaton, B.A.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
D: Pulmonary surfactant-associated protein D
E: Pulmonary surfactant-associated protein D
F: Pulmonary surfactant-associated protein D
G: Pulmonary surfactant-associated protein D
H: Pulmonary surfactant-associated protein D
I: Pulmonary surfactant-associated protein D
J: Pulmonary surfactant-associated protein D
K: Pulmonary surfactant-associated protein D
L: Pulmonary surfactant-associated protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,02348
Polymers190,58012
Non-polymers1,44336
Water22,1941232
1
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)48,00612
Polymers47,6453
Non-polymers3619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-151 kcal/mol
Surface area19050 Å2
MethodPISA
2
D: Pulmonary surfactant-associated protein D
E: Pulmonary surfactant-associated protein D
F: Pulmonary surfactant-associated protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00612
Polymers47,6453
Non-polymers3619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-149 kcal/mol
Surface area18950 Å2
MethodPISA
3
G: Pulmonary surfactant-associated protein D
H: Pulmonary surfactant-associated protein D
I: Pulmonary surfactant-associated protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00612
Polymers47,6453
Non-polymers3619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-148 kcal/mol
Surface area18840 Å2
MethodPISA
4
J: Pulmonary surfactant-associated protein D
K: Pulmonary surfactant-associated protein D
L: Pulmonary surfactant-associated protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00612
Polymers47,6453
Non-polymers3619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-151 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.524, 160.108, 160.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pulmonary surfactant-associated protein D / PSP-D / SP-D / Collectin-7 / Lung surfactant protein D


Mass: 15881.684 Da / Num. of mol.: 12
Fragment: neck and carbohydrate recognition domain (UNP residues 229-375)
Mutation: D325A/R343V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COLEC7, PSPD, SFTP4, SFTPD / Plasmid: pET30A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta blue / References: UniProt: P35247
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1232 / 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: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350) ...Details: Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), 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: May 7, 2012
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: -h,l,k / Fraction: 0.49
ReflectionResolution: 2.096→15 Å / Num. obs: 154671 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.073 / Χ2: 1.443 / Net I/σ(I): 21.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.096-2.174.20.324124821.445178.3
2.17-2.265.40.281148821.492193
2.26-2.365.50.206151321.416194.5
2.36-2.495.60.165154061.445196.3
2.49-2.645.70.138157691.495198.2
2.64-2.855.80.105159361.489199.1
2.85-3.136.10.081160771.471199.8
3.13-3.586.50.068162031.3791100
3.58-4.496.30.056162661.329199.9
4.49-1560.051165181.491199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1063refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G84

3g84


Resolution: 2.096→14.938 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Phase error: 19.15 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 2089 1.35 %RANDOM
Rwork0.1627 ---
obs0.1701 154598 95.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.37 Å2 / Biso mean: 29.934 Å2 / Biso min: 14.48 Å2
Refinement stepCycle: LAST / Resolution: 2.096→14.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12789 0 36 1232 14057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113307
X-RAY DIFFRACTIONf_angle_d0.57218317
X-RAY DIFFRACTIONf_chiral_restr0.041907
X-RAY DIFFRACTIONf_plane_restr0.0052362
X-RAY DIFFRACTIONf_dihedral_angle_d11.9484680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.096-2.14930.28661180.23858533865175
2.1493-2.20730.22051300.226799521008287
2.2073-2.2720.23971420.21105871072993
2.272-2.3450.20191430.2058106551079893
2.345-2.42850.22831420.1989108171095995
2.4285-2.52530.19711400.1962109941113496
2.5253-2.63960.21021490.192111051125497
2.6396-2.77790.20961450.1901111791132498
2.7779-2.95060.24621480.1819113021145098
2.9506-3.17640.20541510.1801113561150799
3.1764-3.49220.20161490.1793113941154399
3.4922-3.98880.17961500.1565114451159599
3.9888-4.99290.15661520.1252114781163098
4.9929-14.76140.13021540.1423116861184098

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