+
Open data
-
Basic information
Entry | Database: PDB / ID: 4wmv | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE OF MBP-MCL1 BOUND TO ligand 4 AT 2.4A | |||||||||
![]() | MBL-MCL1 chimera protein | |||||||||
![]() | APOPTOSIS / protein-protein interaction | |||||||||
Function / homology | ![]() positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / detection of maltose stimulus / maltose transport complex / BH3 domain binding / carbohydrate transport ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / detection of maltose stimulus / maltose transport complex / BH3 domain binding / carbohydrate transport / carbohydrate transmembrane transporter activity / negative regulation of anoikis / maltose binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / maltose transport / maltodextrin transmembrane transport / protein transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex / negative regulation of autophagy / cell chemotaxis / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / outer membrane-bounded periplasmic space / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / periplasmic space / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Clifton, M.C. / Moulin, A. | |||||||||
![]() | ![]() Title: A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1. Authors: Clifton, M.C. / Dranow, D.M. / Leed, A. / Fulroth, B. / Fairman, J.W. / Abendroth, J. / Atkins, K.A. / Wallace, E. / Fan, D. / Xu, G. / Ni, Z.J. / Daniels, D. / Van Drie, J. / Wei, G. / ...Authors: Clifton, M.C. / Dranow, D.M. / Leed, A. / Fulroth, B. / Fairman, J.W. / Abendroth, J. / Atkins, K.A. / Wallace, E. / Fan, D. / Xu, G. / Ni, Z.J. / Daniels, D. / Van Drie, J. / Wei, G. / Burgin, A.B. / Golub, T.R. / Hubbard, B.K. / Serrano-Wu, M.H. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 213.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 165.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 832.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 834.6 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wmrC ![]() 4wmsC ![]() 4wmtC ![]() 4wmuC ![]() 4wmwC ![]() 4wmxC ![]() 4mbpS ![]() 4oq6S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 57310.883 Da / Num. of mol.: 1 / Mutation: K194A, K197A, R201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994, MCL1, BCL2L3 / Production host: ![]() ![]() |
---|---|
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-Non-polymers , 4 types, 148 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/3R4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/3R4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / |
---|---|
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-3R4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.61 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10 MG/ML MBP-MCL1, 200MM MG FORMATE, 20% PEG3350, 1MM MALTOSE, CRYOPROTECTANT 20% ethylene glycol, SOAKED IN 10MM ligand for 2 DAYS |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 20683 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 29.22 Å2 / Rmerge F obs: 0.991 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.157 / Χ2: 0.901 / Net I/σ(I): 10.33 / Num. measured all: 87886 |
Reflection shell | Resolution: 2.4→2.46 Å / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 981 / Num. possible: 289 / Num. unique obs: 272 / Rrim(I) all: 0.034 / Rejects: 0 / % possible all: 99.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4OQ6,4MBP Resolution: 2.4→40 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.64 Å2 / Biso mean: 27.36 Å2 / Biso min: 9.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→40 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|