+Open data
-Basic information
Entry | Database: PDB / ID: 6fcp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of 14-3-3 sigma in complex with Shroom3 P1244L | |||||||||
Components |
| |||||||||
Keywords | PEPTIDE BINDING PROTEIN / Complex | |||||||||
Function / homology | Function and homology information cellular pigment accumulation / pattern specification process / apical protein localization / apical junction complex / cortical actin cytoskeleton / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / epithelial cell development ...cellular pigment accumulation / pattern specification process / apical protein localization / apical junction complex / cortical actin cytoskeleton / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / epithelial cell development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / actin filament organization / adherens junction / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell morphogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / actin filament binding / regulation of cell shape / positive regulation of cell growth / microtubule / cytoskeleton / regulation of cell cycle / cadherin binding / apical plasma membrane / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Leysen, S. / Meijer, F.A. / Milroy, L.G. / Ottmann, C. | |||||||||
Citation | Journal: J. Am. Soc. Nephrol. / Year: 2018 Title: Characterization of Coding/Noncoding Variants forSHROOM3in Patients with CKD. Authors: Prokop, J.W. / Yeo, N.C. / Ottmann, C. / Chhetri, S.B. / Florus, K.L. / Ross, E.J. / Sosonkina, N. / Link, B.A. / Freedman, B.I. / Coppola, C.J. / McDermott-Roe, C. / Leysen, S. / Milroy, L. ...Authors: Prokop, J.W. / Yeo, N.C. / Ottmann, C. / Chhetri, S.B. / Florus, K.L. / Ross, E.J. / Sosonkina, N. / Link, B.A. / Freedman, B.I. / Coppola, C.J. / McDermott-Roe, C. / Leysen, S. / Milroy, L.G. / Meijer, F.A. / Geurts, A.M. / Rauscher, F.J. / Ramaker, R. / Flister, M.J. / Jacob, H.J. / Mendenhall, E.M. / Lazar, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6fcp.cif.gz | 168.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fcp.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fcp_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6fcp_full_validation.pdf.gz | 437 KB | Display | |
Data in XML | 6fcp_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 6fcp_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/6fcp ftp://data.pdbj.org/pub/pdb/validation_reports/fc/6fcp | HTTPS FTP |
-Related structure data
Related structure data | 6fbbC 3lw1S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / Strain (production host): Nico21(DE3) / References: UniProt: P31947 | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 1591.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8TF72 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.18 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES pH7.3 0.19M CaCl2 26% v/v PEG400 5% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→45.55 Å / Num. obs: 51510 / % possible obs: 99.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 12.6 Å2 / Rrim(I) all: 0.074 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2541 / Rrim(I) all: 0.712 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LW1 Resolution: 1.45→45.548 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.1
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→45.548 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|