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- PDB-7zjm: Crystal structure of a complex between CspZ from Borrelia burgdor... -

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Basic information

Entry
Database: PDB / ID: 7zjm
TitleCrystal structure of a complex between CspZ from Borrelia burgdorferi strain B408 and human FH SCR domains 6-7
Components
  • Complement factor H
  • CspZ
KeywordsIMMUNE SYSTEM / Lyme disease / complement system / borreliosis / BBH06.
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / complement component C3b binding / regulation of complement activation / 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 / complement component C3b binding / regulation of complement activation / 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
: / 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
Similarity search - Domain/homology
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Complement factor H
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBrangulis, K. / Marcinkiewicz, A. / Hart, T.M. / Dupuis, A.P. / Zamba Campero, M. / Nowak, T.A. / Stout, J.L. / Akopjana, I. / Kazaks, A. / Bogans, J. ...Brangulis, K. / Marcinkiewicz, A. / Hart, T.M. / Dupuis, A.P. / Zamba Campero, M. / Nowak, T.A. / Stout, J.L. / Akopjana, I. / Kazaks, A. / Bogans, J. / Ciota, A.T. / Kraiczy, P. / Kolokotronis, S.O. / Lin, Y.-P.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other governmentlzp-2020/2-0378 Latvia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural evolution of an immune evasion determinant shapes pathogen host tropism.
Authors: Marcinkiewicz, A.L. / Brangulis, K. / Dupuis 2nd, A.P. / Hart, T.M. / Zamba-Campero, M. / Nowak, T.A. / Stout, J.L. / Akopjana, I. / Kazaks, A. / Bogans, J. / Ciota, A.T. / Kraiczy, P. / ...Authors: Marcinkiewicz, A.L. / Brangulis, K. / Dupuis 2nd, A.P. / Hart, T.M. / Zamba-Campero, M. / Nowak, T.A. / Stout, J.L. / Akopjana, I. / Kazaks, A. / Bogans, J. / Ciota, A.T. / Kraiczy, P. / Kolokotronis, S.O. / Lin, Y.P.
History
DepositionApr 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CspZ
B: Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,74014
Polymers39,8992
Non-polymers84012
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-188 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.098, 71.069, 147.746
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 , 2 types, 2 molecules AB

#1: Protein CspZ


Mass: 25520.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First 4 residues (GAMG) are remnants from the expression tag after TEV protease cleavage. C-terminal region only.
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Strain: B408 / Gene: cspZ / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Complement factor H / H factor 1 / Complement inhibitor factor H SCR domains 6-7


Mass: 14379.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P08603

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Non-polymers , 4 types, 40 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2 M Zinc acetate 0.1 M imidazole (pH 7.4) 10% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97988 Å / Relative weight: 1
ReflectionResolution: 2.59→73.87 Å / Num. obs: 14404 / % possible obs: 99.5 % / Redundancy: 7.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.112 / Net I/σ(I): 12.8
Reflection shellResolution: 2.59→2.71 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1708 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AYD, 4CBE

4ayd

4cbe


Resolution: 2.59→73.87 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.875 / SU B: 11.527 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.659 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 781 5.4 %RANDOM
Rwork0.2176 ---
obs0.2209 13580 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.98 Å2 / Biso mean: 31.914 Å2 / Biso min: 6.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.07 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.59→73.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 34 28 2849
Biso mean--40.5 25.6 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132905
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162690
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6483893
X-RAY DIFFRACTIONr_angle_other_deg1.1921.5896214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2623.397156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56215510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0051513
X-RAY DIFFRACTIONr_chiral_restr0.0660.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
LS refinement shellResolution: 2.592→2.659 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 57 -
Rwork0.27 980 -
all-1037 -
obs--99.42 %

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