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- PDB-2or9: The structure of the anti-c-myc antibody 9E10 Fab fragment/epitop... -

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Basic information

Entry
Database: PDB / ID: 2or9
TitleThe 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
  • (Monoclonal anti-c-myc antibody 9E10) x 2
  • synthetic epitope peptide of 9E10
KeywordsIMMUNE 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 / Transcription of E2F targets under negative control by DREAM complex / response to growth factor / regulation of telomere maintenance / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / negative regulation of gene expression via chromosomal CpG island methylation / branching involved in ureteric bud morphogenesis / Signaling by ALK / E-box binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / chromosome organization / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / : / ERK1 and ERK2 cascade / transcription coregulator binding / positive regulation of epithelial cell proliferation / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / 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 / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / cellular response to UV / MAPK cascade / positive regulation of fibroblast proliferation / cellular response to xenobiotic stimulus / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / intracellular iron ion homeostasis / Estrogen-dependent gene expression / 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 damage response / positive regulation of cell population proliferation / positive regulation of gene expression / protein-containing complex binding / chromatin / nucleolus / 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 / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Myc proto-oncogene protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKrauss, N. / Scheerer, P. / Hoehne, W.
CitationJournal: 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
DepositionFeb 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Monoclonal anti-c-myc antibody 9E10
H: Monoclonal anti-c-myc antibody 9E10
M: Monoclonal anti-c-myc antibody 9E10
I: Monoclonal anti-c-myc antibody 9E10
P: synthetic epitope peptide of 9E10


Theoretical massNumber of molelcules
Total (without water)99,1215
Polymers99,1215
Non-polymers00
Water5,080282
1
L: Monoclonal anti-c-myc antibody 9E10
H: Monoclonal anti-c-myc antibody 9E10
P: synthetic epitope peptide of 9E10


Theoretical massNumber of molelcules
Total (without water)50,2203
Polymers50,2203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Monoclonal anti-c-myc antibody 9E10
I: Monoclonal anti-c-myc antibody 9E10


Theoretical massNumber of molelcules
Total (without water)48,9012
Polymers48,9012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.068, 111.880, 134.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Monoclonal anti-c-myc antibody 9E10


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 Monoclonal anti-c-myc antibody 9E10


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 synthetic epitope peptide of 9E10


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 / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 25, 2000
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CLO

1clo


Resolution: 2.7→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1623 -RANDOM
Rwork0.252 ---
all-31864 --
obs-31864 99.4 %-
Displacement parametersBiso mean: 59.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 0 282 7184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_deg26.645
X-RAY DIFFRACTIONc_improper_angle_deg0.876
LS refinement shellResolution: 2.7→2.8 Å
RfactorNum. reflection% reflection
Rfree0.515 159 -
Rwork0.416 --
obs-3087 97.4 %

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