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Yorodumi- PDB-2or9: The structure of the anti-c-myc antibody 9E10 Fab fragment/epitop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2or9 | ||||||
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Title | The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIGEN-ANTIBODY COMPLEX / ANTIGEN RECOGNITION / myc-tag / long CDR H3 | ||||||
Function / homology | Function and homology information SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / 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 / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / 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 / negative regulation of monocyte differentiation / transcription regulator activator activity / E-box binding / response to growth factor / Transcription of E2F targets under negative control by DREAM complex / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / regulation of telomere maintenance / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / Cyclin E associated events during G1/S transition / negative regulation of gene expression via chromosomal CpG island methylation / branching involved in ureteric bud morphogenesis / Signaling by ALK / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / chromosome organization / core promoter sequence-specific DNA binding / negative regulation of fibroblast proliferation / positive regulation of epithelial cell proliferation / transcription coregulator binding / ERK1 and ERK2 cascade / positive regulation of miRNA transcription / response to gamma radiation / Transcriptional regulation of granulopoiesis / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / MAPK6/MAPK4 signaling / G1/S transition of mitotic cell cycle / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of fibroblast proliferation / cellular response to xenobiotic stimulus / cellular response to UV / MAPK cascade / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / protein dimerization activity / Ub-specific processing proteases / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Krauss, N. / Scheerer, P. / Hoehne, W. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops. Authors: Krauss, N. / Wessner, H. / Welfle, K. / Welfle, H. / Scholz, C. / Seifert, M. / Zubow, K. / Ay, J. / Hahn, M. / Scheerer, P. / Skerra, A. / Hohne, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2or9.cif.gz | 187.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2or9.ent.gz | 149 KB | Display | PDB format |
PDBx/mmJSON format | 2or9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2or9_validation.pdf.gz | 456.7 KB | Display | wwPDB validaton report |
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Full document | 2or9_full_validation.pdf.gz | 489.7 KB | Display | |
Data in XML | 2or9_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 2or9_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/2or9 ftp://data.pdbj.org/pub/pdb/validation_reports/or/2or9 | HTTPS FTP |
-Related structure data
Related structure data | 2orbC 1cloS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24001.543 Da / Num. of mol.: 2 / Fragment: light chain of antigen binding fragment, Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C #2: Antibody | Mass: 24899.799 Da / Num. of mol.: 2 / Fragment: heavy chain of antigen binding fragment, Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C #3: Protein/peptide | | Mass: 1318.407 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: synthetic peptide derived from the human c-myc proto-oncoprotein References: UniProt: P01106*PLUS #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: 2.88 Å3/Da / Density % sol: 57.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 12% PEG 4000, 0.1 to 0.2 M sodium acetate, 0.02% sodium azide, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 25, 2000 |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 31926 / Num. obs: 31926 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 73.2 Å2 / Rsym value: 0.04 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 3088 / Rsym value: 0.25 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CLO Resolution: 2.7→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 59.1 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å
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