+Open data
-Basic information
Entry | Database: PDB / ID: 6akm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SLMAP-SIKE1 complex | ||||||
Components |
| ||||||
Keywords | PROTEIN BINDING / Coiled-coil domain / heterotetramer | ||||||
Function / homology | Function and homology information regulation of membrane depolarization during cardiac muscle cell action potential / regulation of voltage-gated sodium channel activity / regulation of sodium ion transmembrane transport / TRAF6 mediated IRF7 activation / smooth endoplasmic reticulum / muscle contraction / protein localization to plasma membrane / sarcolemma / small GTPase binding / SARS-CoV-1 activates/modulates innate immune responses ...regulation of membrane depolarization during cardiac muscle cell action potential / regulation of voltage-gated sodium channel activity / regulation of sodium ion transmembrane transport / TRAF6 mediated IRF7 activation / smooth endoplasmic reticulum / muscle contraction / protein localization to plasma membrane / sarcolemma / small GTPase binding / SARS-CoV-1 activates/modulates innate immune responses / TRAF3-dependent IRF activation pathway / centrosome / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ma, J. / Chen, M. / Zhou, Z.C. | ||||||
Citation | Journal: Cell Discov / Year: 2019 Title: Architecture, substructures, and dynamic assembly of STRIPAK complexes in Hippo signaling. Authors: Tang, Y. / Chen, M. / Zhou, L. / Ma, J. / Li, Y. / Zhang, H. / Shi, Z. / Xu, Q. / Zhang, X. / Gao, Z. / Zhao, Y. / Cheng, Y. / Jiao, S. / Zhou, Z. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6akm.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6akm.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 6akm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/6akm ftp://data.pdbj.org/pub/pdb/validation_reports/ak/6akm | HTTPS FTP |
---|
-Related structure data
Related structure data | 6akkSC 6aklC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 7184.042 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIKE1, SIKE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Variant (production host): CodonPlus / References: UniProt: Q9BRV8 |
---|---|
#2: Protein | Mass: 7421.357 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLMAP, KIAA1601, SLAP, UNQ1847/PRO3577 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Variant (production host): CodonPlus / References: UniProt: Q14BN4 |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.49 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate, pH 5.5; 15% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 7336 / % possible obs: 100 % / Redundancy: 18.8 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.022 / Rrim(I) all: 0.097 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 19 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 713 / CC1/2: 0.948 / Rpim(I) all: 0.193 / Rrim(I) all: 0.844 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AKK Resolution: 2.3→42.08 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→42.08 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|