+Open data
-Basic information
Entry | Database: PDB / ID: 1nlw | ||||||
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Title | Crystal structure of Mad-Max recognizing DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / transcription factor / DNA / bHLHZ / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information Mad-Max complex / Myc-Max complex / Transcription of E2F targets under negative control by DREAM complex / E-box binding / Transcriptional Regulation by E2F6 / MLL1 complex / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific ...Mad-Max complex / Myc-Max complex / Transcription of E2F targets under negative control by DREAM complex / E-box binding / Transcriptional Regulation by E2F6 / MLL1 complex / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nlw.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nlw.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nlw_validation.pdf.gz | 402.1 KB | Display | wwPDB validaton report |
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Full document | 1nlw_full_validation.pdf.gz | 417.1 KB | Display | |
Data in XML | 1nlw_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1nlw_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nlw ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nlw | HTTPS FTP |
-Related structure data
Related structure data | 1nkpSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5516.579 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Protein | Mass: 9445.983 Da / Num. of mol.: 2 / Fragment: bHLHZ region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Mad / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05195 #3: Protein | Mass: 9121.248 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.95 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% MPD, 5mM magnesium chloride, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 15 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.92 Å |
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Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 35483 / % possible obs: 88.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.052 |
Reflection | *PLUS Num. measured all: 214612 |
Reflection shell | *PLUS % possible obs: 59.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NKP Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |