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Yorodumi- PDB-3t4a: Structure of a truncated form of Staphylococcal Complement Inhibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t4a | ||||||
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Title | Structure of a truncated form of Staphylococcal Complement Inhibitor B bound to human C3c at 3.4 Angstrom resolution | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Age-related macular degeneration / Cleavage on pair of basic residues / Complement alternate pathway / Complement pathway / Disease mutation / Disulfide bond / Glycoprotein / Hemolytic uremic syndrome / Immunity / Inflammatory response / Innate immunity / Phosphoprotein / Secreted / Thioester bond | ||||||
Function / homology | Function and homology information 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 lipid storage / positive regulation of phagocytosis, engulfment ...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 lipid storage / positive regulation of phagocytosis, engulfment / positive regulation of G protein-coupled receptor signaling pathway / 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 / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / fatty acid metabolic process / Peptide ligand-binding receptors / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / 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) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / positive regulation of protein phosphorylation / inflammatory response / 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 | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å | ||||||
Authors | Garcia, B.L. / Geisbrecht, B.V. / Summers, B.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Diversity in the C3b Convertase Contact Residues and Tertiary Structures of the Staphylococcal Complement Inhibitor (SCIN) Protein Family. Authors: Garcia, B.L. / Summers, B.J. / Lin, Z. / Ramyar, K.X. / Ricklin, D. / Kamath, D.V. / Fu, Z.Q. / Lambris, J.D. / Geisbrecht, B.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t4a.cif.gz | 936.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t4a.ent.gz | 774.5 KB | Display | PDB format |
PDBx/mmJSON format | 3t4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t4a_validation.pdf.gz | 509.7 KB | Display | wwPDB validaton report |
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Full document | 3t4a_full_validation.pdf.gz | 652.6 KB | Display | |
Data in XML | 3t4a_validation.xml.gz | 94.4 KB | Display | |
Data in CIF | 3t4a_validation.cif.gz | 126.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/3t4a ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t4a | HTTPS FTP |
-Related structure data
Related structure data | 3t46C 3t47C 3t48C 3t49SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 71393.320 Da / Num. of mol.: 2 / Fragment: C3c beta chain, UNP residues 23-667 / Source method: isolated from a natural source / Details: Human C3 / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 #2: Protein | Mass: 23621.244 Da / Num. of mol.: 2 / Fragment: C3c alpha' chain fragment 1, UNP residues 749-954 / Source method: isolated from a natural source / Details: Human C3 / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 #3: Protein | Mass: 39537.418 Da / Num. of mol.: 2 Fragment: C3c alpha' chain fragment 2, UNP residues 1321-1663 Source method: isolated from a natural source / Details: Human C3 / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 #4: Protein | Mass: 8214.452 Da / Num. of mol.: 2 / Fragment: SCIN-B, UNP residues 49-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: Mu50 / Gene: SAV1159 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99UU9, UniProt: A0A0H3JZ23*PLUS |
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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: 3.04 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 5mg/ml protein, 0.1M bis-Tris, 15% w/v PEG 3350, pH 6.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2010 / Details: MIRROR | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 12.6 % / Av σ(I) over netI: 14.29 / Number: 588795 / Rmerge(I) obs: 0.161 / Χ2: 1 / D res high: 3.4 Å / D res low: 50 Å / Num. obs: 46906 / % possible obs: 97.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 3.4→50 Å / Num. obs: 46906 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 5.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.57 / % possible all: 93.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T49 Resolution: 3.4→32.71 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 0 / Phase error: 25.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.77 Å2 / ksol: 0.29 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.19 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→32.71 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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