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- PDB-6s08: Crystal Structure of Properdin (TSR domains N1 & 456) -

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Entry
Database: PDB / ID: 6s08
TitleCrystal Structure of Properdin (TSR domains N1 & 456)
Components(Properdin) x 2
KeywordsIMMUNE SYSTEM / INNATE IMMUNITY / COMPLEMENT
Function / homology
Function and homology information


cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / specific granule lumen ...cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / specific granule lumen / positive regulation of immune response / tertiary granule lumen / defense response to bacterium / immune response / endoplasmic reticulum lumen / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
: / Thrombospondin type 1 repeat / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
alpha-L-fucopyranose / alpha-D-mannopyranose / TRIETHYLENE GLYCOL / Properdin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
Authorsvan den Bos, R.M. / Pearce, N.M. / Gros, P.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Dutch Kidney Foundation13OCA27 Netherlands
CitationJournal: Front Immunol / Year: 2019
Title: Insights Into Enhanced Complement Activation by Structures of Properdin and Its Complex With the C-Terminal Domain of C3b.
Authors: van den Bos, R.M. / Pearce, N.M. / Granneman, J. / Brondijk, T.H.C. / Gros, P.
History
DepositionJun 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Properdin
B: Properdin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,05514
Polymers36,9502
Non-polymers2,10512
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint10 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.995, 114.860, 39.822
Angle α, β, γ (deg.)90.000, 99.560, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Properdin / / Complement factor P


Mass: 25058.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Cell line (production host): HEK 293ES / Production host: Homo sapiens (human) / References: UniProt: P27918
#2: Protein Properdin / / Complement factor P


Mass: 11891.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Cell line (production host): HEK 293ES / Production host: Homo sapiens (human) / References: UniProt: P27918

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Sugars , 3 types, 10 molecules

#3: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Fucp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-FUC / alpha-L-fucopyranose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 118 molecules

#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Potassium Sulphate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.03→79.61 Å / Num. obs: 17424 / % possible obs: 54.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.66 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.1 / Rrim(I) all: 0.19 / Net I/σ(I): 3.4
Reflection shellResolution: 2.03→2.305 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.249 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 871 / CC1/2: 0.469 / Rpim(I) all: 0.784 / Rrim(I) all: 1.482 / % possible all: 8.7

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Processing

Software
NameVersionClassification
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→79.61 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.881 / SU B: 13.518 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.248
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 879 5 %RANDOM
Rwork0.2117 ---
obs0.2136 16544 54.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.33 Å2 / Biso mean: 29.762 Å2 / Biso min: 8.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.78 Å2
2--0.33 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.03→79.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 130 116 2585
Biso mean--34.92 26.87 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132570
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182137
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.723544
X-RAY DIFFRACTIONr_angle_other_deg1.1941.6265026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8025310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9420.976123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74415341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4261520
X-RAY DIFFRACTIONr_chiral_restr0.0620.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
LS refinement shellResolution: 2.032→2.084 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.23 25 -
obs--1.05 %
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)
13.87163.44271.26533.78771.55141.35290.0071-0.0893-0.1527-0.04920.02-0.0389-0.05970.062-0.02710.02960.01290.00260.05750.01520.02699.868820.94-12.7322
23.9872.5511-2.37522.6333-1.58291.4203-0.0647-0.04970.052-0.05680.0838-0.08810.03330.0288-0.01910.054-0.0499-0.00440.0599-0.0060.0377-32.1018-15.8222-0.5275
32.215-0.1908-0.69841.9347-0.18490.81310.19730.06270.30850.12940.0150.4154-0.0618-0.0604-0.21230.0318-0.00250.06330.03370.00320.1578-52.56991.40929.3495
46.2428-2.1810.5536.11991.24140.4340.0020.0791-0.20050.29730.0846-0.19370.07550.0445-0.08670.0503-0.0237-0.02740.07070.00350.0261-35.5858-24.761914.8237
54.8191-0.2996-0.6894.80341.2271.6497-0.0535-0.18960.04670.08450.01840.1060.0308-0.07230.03510.0129-0.0189-0.00670.05550.01270.0092-14.585215.6078-8.5395
67.999-2.0112-5.87272.53691.70525.33240.0317-0.3290.36220.2570.05890.1485-0.14340.4061-0.09060.0712-0.03160.0450.04550.00680.159-34.595914.80472.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A255 - 312
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A501
4X-RAY DIFFRACTION1A503
5X-RAY DIFFRACTION1A504
6X-RAY DIFFRACTION2A313 - 376
7X-RAY DIFFRACTION2A505
8X-RAY DIFFRACTION2A506
9X-RAY DIFFRACTION3A377 - 415
10X-RAY DIFFRACTION3A430 - 463
11X-RAY DIFFRACTION3A507
12X-RAY DIFFRACTION3A508
13X-RAY DIFFRACTION3A509
14X-RAY DIFFRACTION4A416 - 429
15X-RAY DIFFRACTION5B27 - 76
16X-RAY DIFFRACTION6B77 - 131
17X-RAY DIFFRACTION6B200
18X-RAY DIFFRACTION6B201
19X-RAY DIFFRACTION6B202

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