+Open data
-Basic information
Entry | Database: PDB / ID: 2rod | ||||||
---|---|---|---|---|---|---|---|
Title | Solution Structure of MCL-1 Complexed with NoxaA | ||||||
Components |
| ||||||
Keywords | APOPTOSIS / Mcl-1 / NoxaA / BH3-only / Bcl-2 / Cytoplasm / Developmental protein / Differentiation / Membrane / Mitochondrion / Nucleus / Phosphoprotein / Transmembrane / Ubl conjugation | ||||||
Function / homology | Function and homology information Activation of NOXA and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / BH domain binding / channel activity / fibroblast apoptotic process / mitochondrial fusion ...Activation of NOXA and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / BH domain binding / channel activity / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / T cell homeostasis / BH3 domain binding / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of anoikis / response to X-ray / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to UV / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / regulation of apoptotic process / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | Structure of BH3 domain of the BH3-only protein NoxaA bound to Mcl-1 | ||||||
Authors | Day, C.L. / Smits, C. / Fan, F.C. / Lee, E.F. / Fairlie, W.D. / Hinds, M.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure of the BH3 Domains from the p53-Inducible BH3-Only Proteins Noxa and Puma in Complex with Mcl-1 Authors: Day, C.L. / Smits, C. / Fan, F.C. / Lee, E.F. / Fairlie, W.D. / Hinds, M.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2rod.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2rod.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2rod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rod_validation.pdf.gz | 355.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2rod_full_validation.pdf.gz | 618.2 KB | Display | |
Data in XML | 2rod_validation.xml.gz | 72.6 KB | Display | |
Data in CIF | 2rod_validation.cif.gz | 95.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/2rod ftp://data.pdbj.org/pub/pdb/validation_reports/ro/2rod | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 18260.670 Da / Num. of mol.: 1 / Fragment: residues 152-308 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mcl-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P97287 |
---|---|
#2: Protein/peptide | Mass: 3040.490 Da / Num. of mol.: 1 / Fragment: residues 17-42 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Noxa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q9JM54 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Structure of BH3 domain of the BH3-only protein NoxaA bound to Mcl-1 | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||
NMR details | Text: standard 3D heteronuclear NMR methods were used for resonance assignment |
-Sample preparation
Details |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||
Sample conditions | Ionic strength: 120 mM / pH: 6.7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 Details: The structures were calculated based on a total of 3355 constraints. 2662 are NOE derived and 184 of these are intermolecular. A total of 325 dihedral angle constraints were used and 184 hydrogen bonds. | ||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2662 / NOE intraresidue total count: 849 / NOE long range total count: 725 / NOE medium range total count: 545 / NOE sequential total count: 543 / Hydrogen bond constraints total count: 184 / Protein phi angle constraints total count: 175 / Protein psi angle constraints total count: 150 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 256 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.2 Å | ||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.01 Å / Distance rms dev error: 0.0009 Å |