+Open data
-Basic information
Entry | Database: PDB / ID: 1nkp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Myc-Max recognizing DNA | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION / DNA / bHLHZ / oncogene / heterodimer / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information SCF ubiquitin ligase complex binding / Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors ...SCF ubiquitin ligase complex binding / Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / DNA methylation-dependent heterochromatin formation / negative regulation of monocyte differentiation / Transcription of E2F targets under negative control by DREAM complex / transcription regulator activator activity / response to growth factor / negative regulation of stress-activated MAPK cascade / regulation of telomere maintenance / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / branching involved in ureteric bud morphogenesis / Signaling by ALK / E-box binding / Transcriptional Regulation by E2F6 / MLL1 complex / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / chromosome organization / Cyclin E associated events during G1/S transition / negative regulation of fibroblast proliferation / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of telomerase activity / ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / transcription coregulator binding / protein-DNA complex / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / MAPK6/MAPK4 signaling / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / cellular response to UV / MAPK cascade / positive regulation of fibroblast proliferation / cellular response to xenobiotic stimulus / sequence-specific double-stranded DNA binding / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / intracellular iron ion homeostasis / DNA-binding transcription factor binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / dendrite / DNA damage response / chromatin / positive regulation of cell population proliferation / protein-containing complex binding / nucleolus / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Phased translation search / Resolution: 1.8 Å | ||||||
Authors | Nair, S.K. / Burley, S.K. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: X-ray structures of Myc-Max and Mad-Max recognizing DNA: Molecular bases of regulation by proto-oncogenic transcription factors Authors: Nair, S.K. / Burley, S.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nkp.cif.gz | 136 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nkp.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/1nkp ftp://data.pdbj.org/pub/pdb/validation_reports/nk/1nkp | HTTPS FTP |
---|
-Related structure data
Related structure data | 1nlwC 1an2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 5805.760 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Protein | Mass: 10468.156 Da / Num. of mol.: 2 / Fragment: bHLHZ region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Myc / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01106 #3: Protein | Mass: 9795.012 Da / Num. of mol.: 2 / Fragment: bHLHZ region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Max / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61244 #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.95 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91 Å |
---|---|
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 49228 / % possible obs: 95.9 % / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.053 |
Reflection | *PLUS Num. measured all: 276421 |
Reflection shell | *PLUS % possible obs: 90.9 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: Phased translation search Starting model: PDB ENTRY 1AN2 Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|