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- PDB-4j38: Structure of Borrelia burgdorferi Outer surface protein E in comp... -

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Basic information

Entry
Database: PDB / ID: 4j38
TitleStructure of Borrelia burgdorferi Outer surface protein E in complex with Factor H domains 19-20
Components
  • Complement factor H
  • Outer surface protein E
KeywordsIMMUNE SYSTEM / Beta barrel / Immune Evasion / Complement regulator binding / FH binding / Membrane / ERP PARALOG / LYME DISEASE / BBCRASP-3
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement component C3b binding / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement component C3b binding / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Borrelia outer surface protein E/F / Transcriptional Co-activator pc4; Chain A / : / Complement Module, domain 1 / Complement Module; domain 1 / 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 ...Borrelia outer surface protein E/F / Transcriptional Co-activator pc4; Chain A / : / Complement Module, domain 1 / Complement Module; domain 1 / 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 / Ribbon / Roll / Mainly Beta
Similarity search - Domain/homology
: / Complement factor H
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsBhattacharjee, A. / Kolodziejczyk, R. / Kajander, T. / Goldman, A. / Jokiranta, T.S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for Complement Evasion by Lyme Disease Pathogen Borrelia burgdorferi
Authors: Bhattacharjee, A. / Oeemig, J.S. / Kolodziejczyk, R. / Meri, T. / Kajander, T. / Lehtinen, M.J. / Iwai, H. / Jokiranta, T.S. / Goldman, A.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer surface protein E
B: Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6533
Polymers31,5572
Non-polymers961
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-14 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.405, 86.405, 107.784
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Outer surface protein E


Mass: 16941.975 Da / Num. of mol.: 1 / Fragment: UNP residues 21-171
Source method: isolated from a genetically manipulated source
Details: Surface protein
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: N40 / Gene: OspE / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: E4QGX1
#2: Protein Complement factor H / H factor 1


Mass: 14614.674 Da / Num. of mol.: 1 / Fragment: FH domains 19-20, UNP residues 1103-1231 / Mutation: D1119G, Q1139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH / Plasmid: pPICZalphaB / Production host: Komagataella pastoris (fungus) / References: UniProt: P08603
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.68 Å3/Da / Density % sol: 66.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2M Ammonium sulfate, 0.1M Citric acid, 0.2M Sodium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2011
RadiationMonochromator: ESRF monochromator and torodial focusing mirro
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97372 Å / Relative weight: 1
ReflectionResolution: 2.83→50 Å / Num. obs: 12063 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.05 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.88
Reflection shellResolution: 2.83→2.9 Å / Redundancy: 7.08 % / Rmerge(I) obs: 1.098 / Mean I/σ(I) obs: 2.2 / % possible all: 95.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
Rosettamodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2G7I

2g7i


Resolution: 2.83→19.509 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7954 / SU ML: 0.92 / σ(F): 2.01 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 573 5 %RANDOM
Rwork0.1933 ---
obs0.1964 11456 99.93 %-
all-12063 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.298 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 168.12 Å2 / Biso mean: 64.8 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-9.5214 Å20 Å2-0 Å2
2--9.5214 Å20 Å2
3----19.0428 Å2
Refinement stepCycle: LAST / Resolution: 2.83→19.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 5 15 1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121968
X-RAY DIFFRACTIONf_angle_d1.3722668
X-RAY DIFFRACTIONf_chiral_restr0.091300
X-RAY DIFFRACTIONf_plane_restr0.006342
X-RAY DIFFRACTIONf_dihedral_angle_d18.36689
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8302-3.1140.35251400.292226632803
3.114-3.56220.26111420.213926952837
3.5622-4.4790.2281420.157427052847
4.479-19.50960.24151490.184128202969
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)
15.6813-0.05671.60682.36460.30592.3187-0.1443-1.3032-0.63150.1160.32220.0740.2274-0.7092-0.11410.31570.04180.08180.81260.21630.4518-12.861932.9013-3.2797
29.3123-3.34763.31671.2646-0.85296.42620.8705-0.4112-0.6742-0.1656-0.10560.0612.140.8762-0.84480.85170.0437-0.18710.53060.01650.500527.500523.671320.4475
32.51-1.23031.90963.5939-0.05552.3747-0.04350.2163-0.10120.8083-0.0817-0.43970.86670.78160.0490.76970.1741-0.0720.37480.00370.427920.435328.934520.2375
47.36561.10573.13566.9111-3.29273.6492-0.63090.7720.25140.6032-0.14170.5890.26290.09850.30270.49730.2047-0.0030.4453-0.12330.451712.401534.75129.3303
56.117-4.97553.74336.5745-3.99433.1795-0.04610.587-0.15940.1693-0.12250.06860.81780.43320.3780.81020.3359-0.05760.4689-0.0690.404119.025225.435811.4374
60.80370.12470.25333.0401-2.28812.9736-1.38141.39851.4614-0.03150.0656-0.947-1.17441.42241.10490.6063-0.2269-0.27780.77490.28721.0037.109951.8407-8.5289
75.94990.53591.42172.47920.00653.0072-0.7616-0.36831.00020.29550.313-0.6459-0.8659-0.29730.45770.29410.0132-0.13060.52470.04310.59270.512944.7473-4.1812
83.0908-0.85820.06386.74930.64392.15670.0461.35660.7708-1.618-0.6498-0.6005-0.24960.78890.54380.61350.1199-0.08060.81750.16970.53494.665643.866-14.0452
94.1931-3.89833.06164.5237-3.65914.4276-0.66880.241-0.2726-0.8175-0.019-1.24240.31170.57940.57450.4327-0.32240.03591.09130.28160.83887.105146.1166-14.5806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 40:171)A40 - 171
2X-RAY DIFFRACTION2(chain B and resid 1106:1114)B1106 - 1114
3X-RAY DIFFRACTION3(chain B and resid 1115:1134)B1115 - 1134
4X-RAY DIFFRACTION4(chain B and resid 1135:1145)B1135 - 1145
5X-RAY DIFFRACTION5(chain B and resid 1146:1166)B1146 - 1166
6X-RAY DIFFRACTION6(chain B and resid 1167:1179)B1167 - 1179
7X-RAY DIFFRACTION7(chain B and resid 1180:1200)B1180 - 1200
8X-RAY DIFFRACTION8(chain B and resid 1201:1223)B1201 - 1223
9X-RAY DIFFRACTION9(chain B and resid 1224:1228)B1224 - 1228

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