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- PDB-6s0a: Crystal Structure of Properdin (TSR domains N12 & 456) -

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Basic information

Entry
Database: PDB / ID: 6s0a
TitleCrystal Structure of Properdin (TSR domains N12 & 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 / Properdin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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.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.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Properdin
B: Properdin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,08716
Polymers43,0452
Non-polymers3,04314
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint18 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.753, 114.753, 232.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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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: 17986.215 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 , 4 types, 14 molecules

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


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-Glycam 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
[]{[(3+1)][a-L-Fucp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 10
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
#6: 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 , 1 types, 11 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 4.44 Å3/Da / Density % sol: 72.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Sodium Citrate, PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.516→102.881 Å / Num. obs: 16212 / % possible obs: 60.5 % / Redundancy: 8.8 % / Biso Wilson estimate: 50.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.063 / Rrim(I) all: 0.196 / Net I/σ(I): 7.5
Reflection shellResolution: 2.516→2.709 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.639 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 810 / CC1/2: 0.629 / Rpim(I) all: 0.522 / Rrim(I) all: 1.722 / % possible all: 15.5

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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: 2.52→102.881 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.885 / SU B: 27.828 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.654 / ESU R Free: 0.35
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 770 4.7 %RANDOM
Rwork0.248 ---
obs0.2489 15443 60.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 144.09 Å2 / Biso mean: 64.017 Å2 / Biso min: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å2-0 Å20 Å2
2--1.39 Å20 Å2
3----2.79 Å2
Refinement stepCycle: final / Resolution: 2.52→102.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 190 11 2906
Biso mean--76.76 32.57 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133014
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182444
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.7454172
X-RAY DIFFRACTIONr_angle_other_deg1.2581.6515748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.545365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.34120.735136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69815372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4421523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02609
LS refinement shellResolution: 2.516→2.581 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.54 7 -
Rwork0.486 114 -
all-121 -
obs--6.2 %
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)
17.83210.63692.30930.82450.0490.7111-0.0744-0.08590.0165-0.05040.03930.0322-0.0115-0.03430.03510.0047-0.00210.0160.0038-0.00340.23612.309-47.7118-50.4364
27.9393-2.5277-0.91951.26960.37240.142-0.038-0.0849-0.1770.07740.0120.02210.00690.01880.02590.0157-0.0079-0.03540.00840.02430.2646-43.1744-38.6055-43.4831
34.18882.9896-0.23622.7363-0.05141.09240.37-0.43420.23750.5952-0.21630.1196-0.05110.0943-0.15370.22940.0168-0.02450.0718-0.07390.1643-43.0091-11.1703-34.9866
40.1530.4469-0.97265.8055-2.10889.5404-0.1879-0.0277-0.00530.2680.7383-0.01950.42480.2815-0.55040.41330.12240.06360.26990.11040.254-51.0775-41.1344-28.3034
52.70569.76025.091335.759318.74089.86770.0856-0.27970.3842-0.1588-0.991.5051-0.1293-0.55540.90430.41840.02570.02140.3245-0.04790.4102-10.3039-18.0188-43.4015
63.56970.12492.96864.75312.0694.7979-0.21140.03490.1429-0.0883-0.120.1522-0.5184-0.18520.33130.08270.0378-0.0010.0415-0.0120.339-8.1032-34.8442-44.9834
71.70290.6402-0.42978.22166.09745.0873-0.1965-0.2613-0.17690.53030.3616-0.21850.53960.5671-0.16510.32410.2588-0.11820.4199-0.15690.2366-21.0835-16.954-38.6324
84.8139-0.06782.40570.96080.31011.4088-0.222-1.15810.1482-0.2653-0.13110.0644-0.3933-0.61030.35311.0715-0.1315-0.10291.2227-0.01360.855-2.139520.4012-10.7958
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A254 - 312
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A501
4X-RAY DIFFRACTION1A502 - 503
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 DIFFRACTION4A510
16X-RAY DIFFRACTION4A511
17X-RAY DIFFRACTION5A464 - 471
18X-RAY DIFFRACTION6B27 - 76
19X-RAY DIFFRACTION7B77 - 131
20X-RAY DIFFRACTION7B200
21X-RAY DIFFRACTION7B201
22X-RAY DIFFRACTION7B202
23X-RAY DIFFRACTION8B132 - 190
24X-RAY DIFFRACTION8B203
25X-RAY DIFFRACTION8B204
26X-RAY DIFFRACTION8B205

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