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- PDB-6s0b: Crystal Structure of Properdin in complex with the CTC domain of ... -

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Basic information

Entry
Database: PDB / ID: 6s0b
TitleCrystal Structure of Properdin in complex with the CTC domain of C3/C3b
Components
  • (Properdin) x 2
  • Complement C3
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 / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance ...cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / specific granule lumen / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / azurophil granule lumen / tertiary granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / defense response to bacterium / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Thrombospondin type 1 repeat / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. ...: / Thrombospondin type 1 repeat / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin-like fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Complement C3 / Properdin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.312 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.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 / _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
C: Complement C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,21413
Polymers54,2253
Non-polymers1,98910
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint2 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.471, 71.497, 134.182
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#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
#3: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 17275.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Cell line (production host): HEK 293ES / Production host: Homo sapiens (human) / References: UniProt: P01024

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Sugars , 3 types, 10 molecules

#4: 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-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
#5: Sugar
ChemComp-MAN / alpha-D-mannopyranose


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
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 70 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Tacsimate, 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 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.312→63.081 Å / Num. obs: 21145 / % possible obs: 68.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 47.02 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.047 / Rrim(I) all: 0.111 / Net I/σ(I): 11.1
Reflection shellResolution: 2.312→2.601 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.267 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1538 / CC1/2: 0.56 / Rpim(I) all: 0.637 / Rrim(I) all: 1.426 / % possible all: 17.1

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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: 2.312→48.96 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.888 / SU B: 25.389 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.499 / ESU R Free: 0.315
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 1069 5.1 %RANDOM
Rwork0.2298 ---
obs0.2323 20068 67.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 148.91 Å2 / Biso mean: 52.826 Å2 / Biso min: 26.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å2-0 Å2
2---1.09 Å2-0 Å2
3---2.85 Å2
Refinement stepCycle: final / Resolution: 2.312→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 123 70 3623
Biso mean--58.33 40.23 -
Num. residues----461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133695
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183099
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.6975072
X-RAY DIFFRACTIONr_angle_other_deg1.1891.6157238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2755459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16621.834169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83515508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5151523
X-RAY DIFFRACTIONr_chiral_restr0.0560.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02755
LS refinement shellResolution: 2.303→2.363 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 4 -
Rwork0.315 54 -
all-58 -
obs--2.63 %
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)
11.94420.753-0.24692.5121-3.004210.60960.00110.1685-0.00180.26720.1290.126-0.06130.0831-0.13010.1791-0.01410.00180.04630.0070.009111.5477-27.218881.712
21.35092.5094-2.82114.8329-5.15356.59010.0331-0.1369-0.1567-0.0628-0.0729-0.3104-0.15330.17080.03980.3054-0.0257-0.00140.32180.07340.139824.00698.135139.7077
31.5449-0.19460.9472.2967-2.09064.2957-0.0971-0.10040.25180.3638-0.2612-0.3469-0.82460.8670.35830.4468-0.2641-0.07220.4058-0.02490.096449.930916.19348.8592
41.8528-2.83763.39578.0022-4.102510.0735-0.0618-0.69220.02760.79840.13010.9569-0.7115-1.0775-0.06820.5889-0.14720.25140.6207-0.32060.349819.014325.218336.5322
50.5143-1.05611.25624.28330.109312.6642-0.0295-0.0825-0.49880.57090.66380.4879-0.42870.0357-0.63430.48680.0432-0.2640.4239-0.07880.925644.2942-8.190476.3053
64.891-0.08051.29794.154-1.15315.17470.1002-0.296-0.36530.09910.36270.4564-0.1429-0.6718-0.46290.27490.06850.05960.31960.13910.10673.72778.339327.7378
75.95652.0961-0.38542.222-2.08157.26320.0469-0.23920.11850.1042-0.10330.0525-0.07370.28780.05630.10690.0092-0.00530.17320.00530.004624.4639-13.206669.0868
87.99556.86850.77137.6868-0.49113.1230.074-0.47910.51450.5-0.23210.4698-0.49320.05760.15810.19890.0258-0.00140.2225-0.03110.041939.13370.786763.2373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A254 - 312
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A502
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 DIFFRACTION3A508
12X-RAY DIFFRACTION3A509
13X-RAY DIFFRACTION3A510
14X-RAY DIFFRACTION4A416 - 429
15X-RAY DIFFRACTION4A507
16X-RAY DIFFRACTION5A464 - 471
17X-RAY DIFFRACTION6C1516 - 1663
18X-RAY DIFFRACTION7B27 - 76
19X-RAY DIFFRACTION8B77 - 127
20X-RAY DIFFRACTION8B200

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