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- PDB-5nbq: The structure of the tripartite complex between OspE, the C-termi... -

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Basic information

Entry
Database: PDB / ID: 5nbq
TitleThe structure of the tripartite complex between OspE, the C-terminal domains of factor H and C3dg
Components
  • Complement C3Complement component 3
  • Complement factor HFactor H
  • Outer surface protein E
  • Outer surface protein E,Outer surface protein E
KeywordsIMMUNE SYSTEM / complement / regulation / microbe / evasion
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C3b binding / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance ...regulation of complement activation, alternative pathway / symbiont cell surface / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C3b binding / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / 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 / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / 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 / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / response to bacterium / Post-translational protein phosphorylation / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / azurophil granule lumen / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / heparin binding / G alpha (i) signalling events / secretory granule lumen / blood microparticle / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Borrelia outer surface protein E/F / OspE-like superfamily / Borrelia outer surface protein E / Borrelia outer surface protein E/F / Transcriptional Co-activator pc4; Chain A / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain ...Borrelia outer surface protein E/F / OspE-like superfamily / Borrelia outer surface protein E / Borrelia outer surface protein E/F / Transcriptional Co-activator pc4; Chain A / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement Module, domain 1 / 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 / Complement Module; domain 1 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / 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 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Ribbon / Roll / Immunoglobulin-like fold / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Complement C3 / Complement factor H / Outer surface protein E
Similarity search - Component
Biological speciesHomo sapiens (human)
Borreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.18 Å
AuthorsKolodziejczyk, R. / Mikula, K.M. / Kotila, T.M. / Postis, V.L.G. / Sakari, J.T. / Meri, T.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland255922 and 259793 Finland
Sigrid Juselius Foundation Finland
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structure of a tripartite complex between C3dg, C-terminal domains of factor H and OspE of Borrelia burgdorferi.
Authors: Kolodziejczyk, R. / Mikula, K.M. / Kotila, T. / Postis, V.L.G. / Jokiranta, T.S. / Goldman, A. / Meri, T.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3
B: Complement C3
C: Complement C3
D: Complement factor H
E: Complement factor H
F: Complement factor H
G: Outer surface protein E
H: Outer surface protein E,Outer surface protein E
I: Outer surface protein E


Theoretical massNumber of molelcules
Total (without water)185,3859
Polymers185,3859
Non-polymers00
Water362
1
A: Complement C3
D: Complement factor H
G: Outer surface protein E


Theoretical massNumber of molelcules
Total (without water)61,6533
Polymers61,6533
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C3
E: Complement factor H
H: Outer surface protein E,Outer surface protein E


Theoretical massNumber of molelcules
Total (without water)62,0793
Polymers62,0793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement C3
F: Complement factor H
I: Outer surface protein E


Theoretical massNumber of molelcules
Total (without water)61,6533
Polymers61,6533
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.907, 165.063, 84.185
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 32824.590 Da / Num. of mol.: 3 / Mutation: A1153E, C1010A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01024
#2: Protein Complement factor H / Factor H / H factor 1


Mass: 14443.388 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Production host: Pichia (fungus) / References: UniProt: P08603
#3: Protein Outer surface protein E


Mass: 14385.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: OspE / Production host: Escherichia coli (E. coli) / References: UniProt: Q45001
#4: Protein Outer surface protein E,Outer surface protein E


Mass: 14810.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: OspE / Production host: Escherichia coli (E. coli) / References: UniProt: Q45001
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M MgCl2 or 24% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M MgCl2 or 16% PEG3350, Tris pH 8.5, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 3.18→29.6 Å / Num. obs: 29070 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.419 % / Biso Wilson estimate: 78.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.147 / Χ2: 1.038 / Net I/σ(I): 12.43 / Num. measured all: 186599
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.18-3.375.3990.8921.7321040473638970.670.98382.3
3.37-3.66.740.5663.3629611440243930.8710.61499.8
3.6-3.886.6970.3455.5827898416741660.9470.374100
3.88-4.256.6890.1979.4325721385138450.9810.21499.8
4.25-4.746.5910.11914.9823068350235000.9920.12999.9
4.74-5.456.6410.117.3720734312331220.9940.108100
5.45-6.616.4420.09817.417238267626760.9940.107100
6.61-9.136.3390.0531.3413471213121250.9990.05599.7
9.13-29.65.8080.03344.897818140213460.9990.03696

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→29.6 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.519
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1406 4.84 %RANDOM
Rwork0.233 ---
obs0.235 29068 97.1 %-
Displacement parametersBiso max: 287.66 Å2 / Biso mean: 91.13 Å2 / Biso min: 20.15 Å2
Baniso -1Baniso -2Baniso -3
1-8.005 Å20 Å20 Å2
2---17.3466 Å20 Å2
3---9.3416 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 3.18→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11752 0 0 2 11754
Biso mean---75.25 -
Num. residues----1504
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4142SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes317HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1709HARMONIC5
X-RAY DIFFRACTIONt_it12011HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1561SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13741SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12011HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg16276HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion19.86
LS refinement shellResolution: 3.18→3.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.245 90 4.37 %
Rwork0.2602 1971 -
all0.2596 2061 -
obs--71.21 %
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)
12.3054-0.9082-0.92033.69741.80222.63050.0523-0.45040.38680.03680.2375-0.4992-0.12540.5422-0.2897-0.04390.08330.0917-0.0711-0.0391-0.128444.472230.47439.1732
22.1517-0.18630.33252.0951-0.35851.96360.04-0.25-0.38920.00710.18520.5442-0.0145-0.3822-0.2251-0.1356-0.0438-0.0161-0.07830.11770.096335.9521-1.732414.5549
32.40230.47940.4152.45820.37082.06830.09180.1060.43460.2075-0.00190.1013-0.1323-0.2154-0.0899-0.15820.01260.0217-0.04960.13110.056716.773118.4172-14.7699
41.67580.82380.24354.4590.78090.07580.0429-0.26450.0756-0.16310.0060.0909-0.0904-0.097-0.04890.07820.11340.0821-0.0694-0.0074-0.050513.953728.580546.6692
54.4204-1.49412.50573.4837-0.46572.6858-0.0922-0.01710.5352-0.1850.16980.2568-0.2107-0.0583-0.0776-0.0312-0.04190.0566-0.1018-0.0064-0.012152.19224.577715.9792
66.22420.3991-2.72680.1328-0.1933.476-0.009-0.207-0.25840.1130.165-0.05210.2757-0.0383-0.156-0.1193-0.152-0.1382-0.10710.03540.15327.4052-9.7384-8.5794
73.4481-1.57421.08121.3259-0.69954.53940.07390.27160.1327-0.2020.00170.2903-0.021-0.1584-0.0756-0.04060.1520.00690.16690.0227-0.26141.185723.783324.6374
82.0468-0.225-2.89034.80432.54265.9061-0.0665-0.01470.01280.15770.078-0.09490.12260.0693-0.01160.0215-0.0597-0.0975-0.17780.01990.015540.0573-23.1729-29.3408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A996 - 1285
2X-RAY DIFFRACTION2{ B|* }B995 - 1287
3X-RAY DIFFRACTION3{ C|* }C994 - 1286
4X-RAY DIFFRACTION4{ D|* }D1104 - 1230
5X-RAY DIFFRACTION5{ E|* }E1105 - 1229
6X-RAY DIFFRACTION6{ F|* }F1106 - 1228
7X-RAY DIFFRACTION7{ G|* }G42 - 170
8X-RAY DIFFRACTION8{ I|* }I42 - 170

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