[English] 日本語
Yorodumi- PDB-2vxs: Structure of IL-17A in complex with a potent, fully human neutral... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 2vxs | ||||||
|---|---|---|---|---|---|---|---|
| Title | Structure of IL-17A in complex with a potent, fully human neutralising antibody | ||||||
Components |
| ||||||
Keywords | CYTOKINE / EPITOPE / COMPLEX / ANTIBODY / SECRETED / GLYCOPROTEIN / INTERLEUKIN-17 | ||||||
| Function / homology | Function and homology informationpositive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / intestinal epithelial structure maintenance / fibroblast activation / positive regulation of bicellular tight junction assembly / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / cytokine activity / positive regulation of interleukin-1 beta production / positive regulation of interleukin-6 production / response to wounding / positive regulation of tumor necrosis factor production / cell-cell signaling / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / gene expression / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / innate immune response / external side of plasma membrane / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
| Biological species | HOMO SAPIENS (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | ||||||
Authors | Gerhardt, S. / Hargreaves, D. / Pauptit, R.A. / Davies, R.A. / Russell, C. / Welsh, F. / Tuske, S.J. / Coales, S.J. / Hamuro, Y. / Needham, M.R.C. ...Gerhardt, S. / Hargreaves, D. / Pauptit, R.A. / Davies, R.A. / Russell, C. / Welsh, F. / Tuske, S.J. / Coales, S.J. / Hamuro, Y. / Needham, M.R.C. / Langham, C. / Barker, W. / Bell, P. / Aziz, A. / Smith, M.J. / Dawson, S. / Abbott, W.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009Title: Structure of Il-17A in Complex with a Potent, Fully Human Neutralising Antibody. Authors: Gerhardt, S. / Abbott, W.M. / Hargreaves, D. / Pauptit, R.A. / Davies, R.A. / Needham, M.R. / Langham, C. / Barker, W. / Aziz, A. / Snow, M.J. / Dawson, S. / Welsh, F. / Wilkinson, T. / ...Authors: Gerhardt, S. / Abbott, W.M. / Hargreaves, D. / Pauptit, R.A. / Davies, R.A. / Needham, M.R. / Langham, C. / Barker, W. / Aziz, A. / Snow, M.J. / Dawson, S. / Welsh, F. / Wilkinson, T. / Vaugan, T. / Beste, G. / Bishop, S. / Popovic, B. / Rees, G. / Sleeman, M. / Tuske, S.J. / Coales, S.J. / Hamuro, Y. / Russell, C. | ||||||
| History |
| ||||||
| Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 2vxs.cif.gz | 393.3 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb2vxs.ent.gz | 320.1 KB | Display | PDB format |
| PDBx/mmJSON format | 2vxs.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2vxs_validation.pdf.gz | 536.2 KB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 2vxs_full_validation.pdf.gz | 577.4 KB | Display | |
| Data in XML | 2vxs_validation.xml.gz | 69.9 KB | Display | |
| Data in CIF | 2vxs_validation.cif.gz | 97.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/2vxs ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vxs | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 1aqkS S: Starting model for refinement |
|---|---|
| Similar structure data |
-
Links
-
Assembly
| Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-
Components
| #1: Protein | Mass: 15689.864 Da / Num. of mol.: 4 / Fragment: RESIDUES 20-155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PT7 / Production host: ![]() #2: Antibody | Mass: 23671.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ![]() #3: Antibody | Mass: 23196.564 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ![]() #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has protein modification | Y | Sequence details | SWISSPROT ACCESSION NUMBER Q16552. THE NUMBERING OF THE FAB-FRAGMENT (CHAINS H,I,J,K AND L,M,N,O) ...SWISSPROT ACCESSION NUMBER Q16552. THE NUMBERING OF THE FAB-FRAGMENT (CHAINS H,I,J,K AND L,M,N,O) ARE ACCORDING TO THE NOMENCLATU | |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54 % / Description: NONE |
|---|---|
| Crystal grow | Details: 90.9 MM PCTP BUFFER PH 4.0, 9.1 MM PCTP BUFFER PH 9.5, 100 MM AMMONIUM SULPHATE, 14% W/V PEG3350 |
-Data collection
| Diffraction | Mean temperature: 100 K |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9787 |
| Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 30, 2007 / Details: TOROIDAL MIRROR |
| Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
| Reflection | Resolution: 2.63→102.1 Å / Num. obs: 79235 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.7 |
| Reflection shell | Resolution: 2.63→2.77 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1AQK Resolution: 2.63→204.12 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.868 / SU B: 24.577 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.635 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 19.75 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.63→204.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi



HOMO SAPIENS (human)
X-RAY DIFFRACTION
Citation










PDBj









