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Yorodumi- PDB-4aym: Structure of a complex between CCPs 6 and 7 of Human Complement F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aym | ||||||
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Title | Structure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria meningitidis FHbp Variant 3 P106A mutant | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIGENS / VACCINES | ||||||
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 / 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 MC58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Johnson, S. / Tan, L. / van der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Everett, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. ...Johnson, S. / Tan, L. / van der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Everett, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / Newham, L. / Staunton, D. / Borrow, R. / Pickering, M. / Lea, S.M. / Tang, C.M. | ||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: Design and Evaluation of Meningococcal Vaccines Through Structure-Based Modification of Host and Pathogen Molecules. Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / ...Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / Newham, L. / Staunton, D. / Ufret-Vincenty, R. / Borrow, R. / Pickering, M.C. / Lea, S.M. / Tang, C.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" 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 "DB" 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aym.cif.gz | 197.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aym.ent.gz | 157.7 KB | Display | PDB format |
PDBx/mmJSON format | 4aym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aym_validation.pdf.gz | 470.2 KB | Display | wwPDB validaton report |
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Full document | 4aym_full_validation.pdf.gz | 473 KB | Display | |
Data in XML | 4aym_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 4aym_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/4aym ftp://data.pdbj.org/pub/pdb/validation_reports/ay/4aym | HTTPS FTP |
-Related structure data
Related structure data | 2ybyC 4aydC 4ayeC 4ayiC 4aynC 2w81S 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 14410.275 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: HIS402 POLYMORPHISM / Plasmid: PET-14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): B834(DE3) / References: UniProt: P08603 #2: Protein | Mass: 29487.807 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-281 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA MENINGITIDIS MC58 (bacteria) / Variant: P28 / Plasmid: PET-14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): B834(DE3) / References: UniProt: Q19KF7 #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | THIS IS THE HIS402 POLYMORPHISM. MG AT THE START COME FROM THE VECTOR. DISCREPANCIES AT TERMINII ...THIS IS THE HIS402 POLYMORPHI | |
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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: 2.53 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 0.2 M IMIDAZOLE PH 6, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→180 Å / Num. obs: 28212 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 73.84 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.85→2.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W81 Resolution: 3→15 Å / Cor.coef. Fo:Fc: 0.8502 / Cor.coef. Fo:Fc free: 0.8691 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.418 Details: NUMBER OF RESTRAINT LIBRARIES USED: 7 REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 56.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.538 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.13 Å / Total num. of bins used: 12
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