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Yorodumi- PDB-2w80: Structure of a complex between Neisseria meningitidis factor H bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w80 | ||||||
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Title | Structure of a complex between Neisseria meningitidis factor H binding protein and CCPs 6-7 of human complement factor H | ||||||
Components |
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Keywords | IMMUNE SYSTEM / GLYCOPROTEIN / IMMUNE EVASION / AGE-RELATED MACULAR DEGENERATION / INNATE IMMUNITY / IMMUNE RESPONSE / DISEASE MUTATION / FACTOR H / COMPLEMENT ALTERNATE PATHWAY / VACCINE CANDIDATE | ||||||
Function / homology | Function and homology information regulation of complement activation, alternative pathway / bacterial extracellular vesicle / 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 activation, alternative pathway / bacterial extracellular vesicle / 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 / cell outer membrane / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) NEISSERIA MENINGITIDIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Schneider, M.C. / Prosser, B.E. / Caesar, J.J.E. / Kugelberg, E. / Li, S. / Zhang, Q. / Quoraishi, S. / Lovett, J.E. / Deane, J.E. / Sim, R.B. ...Schneider, M.C. / Prosser, B.E. / Caesar, J.J.E. / Kugelberg, E. / Li, S. / Zhang, Q. / Quoraishi, S. / Lovett, J.E. / Deane, J.E. / Sim, R.B. / Roversi, P. / Johnson, S. / Tang, C.M. / Lea, S.M. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Neisseria Meningitidis Recruits Factor H Using Protein Mimicry of Host Carbohydrates. Authors: Schneider, M.C. / Prosser, B.E. / Caesar, J.J.E. / Kugelberg, E. / Li, S. / Zhang, Q. / Quoraishi, S. / Lovett, J.E. / Deane, J.E. / Sim, R.B. / Roversi, P. / Johnson, S. / Tang, C.M. / Lea, S.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w80.cif.gz | 300 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w80.ent.gz | 243.1 KB | Display | PDB format |
PDBx/mmJSON format | 2w80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w80_validation.pdf.gz | 490 KB | Display | wwPDB validaton report |
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Full document | 2w80_full_validation.pdf.gz | 534.9 KB | Display | |
Data in XML | 2w80_validation.xml.gz | 61.9 KB | Display | |
Data in CIF | 2w80_validation.cif.gz | 86.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/2w80 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w80 | HTTPS FTP |
-Related structure data
Related structure data | 2w81C 2uwnS S: Starting model for refinement C: citing same article (ref.) |
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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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 14222.026 Da / Num. of mol.: 4 / Fragment: CCPS 6 AND 7, RESIDUES 321-443 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Variant: HIS 402 FORM / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08603 #2: Protein | Mass: 26983.078 Da / Num. of mol.: 4 Fragment: FULL PROTEIN WITHOUT SIGNAL SEQUENCE, RESIDUES 71-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JXV4 #3: Water | ChemComp-HOH / | Sequence details | FRAGMENT OF THIS ENTRY -CCPS 6 AND 7 ONLY | |
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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: 2.64 Å3/Da / Density % sol: 53.06 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 20% PEG 6000, 0.1M BICINE PH9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9523 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9523 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→95 Å / Num. obs: 64754 / % possible obs: 91.3 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 50.27 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.1 / % possible all: 80.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UWN Resolution: 2.35→95 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE 4 COPIES OF THE COMPLEX IN THE ASYMMETRIC UNIT, BUT SUBTLE REARRANGMENTS MEAN THAT NCS WAS NOT USED IN THE FINAL REFINEMENT
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Displacement parameters | Biso mean: 40.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→95 Å
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LS refinement shell | Resolution: 2.35→2.49 Å / Total num. of bins used: 9
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