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Yorodumi- PDB-7zjm: Crystal structure of a complex between CspZ from Borrelia burgdor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zjm | ||||||
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Title | Crystal structure of a complex between CspZ from Borrelia burgdorferi strain B408 and human FH SCR domains 6-7 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Lyme disease / complement system / borreliosis / BBH06. | ||||||
Function / homology | Function and homology information regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Borreliella burgdorferi (Lyme disease spirochete) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | 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. ...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
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zjm.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zjm.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 7zjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/7zjm ftp://data.pdbj.org/pub/pdb/validation_reports/zj/7zjm | HTTPS FTP |
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-Related structure data
Related structure data | 7zjjC 7zjkC 4aydS 4cbeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | 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) |
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#2: Protein | 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 |
-Non-polymers , 4 types, 40 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-IMD / #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.22 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97988 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97988 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.98 Å2 / Biso mean: 31.914 Å2 / Biso min: 6.91 Å2
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Refinement step | Cycle: final / Resolution: 2.59→73.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.592→2.659 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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