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- PDB-1jky: Crystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF... -
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Basic information
Entry | Database: PDB / ID: 1jky | ||||||
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Title | Crystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF Complexed with the N-terminal Sequence of MAPKK2 | ||||||
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![]() | TOXIN / Lethal Toxin / Mek2 / MAPKK / Uncleaved substrate / Protease-substrate complex | ||||||
Function / homology | ![]() anthrax lethal factor endopeptidase / epithelial cell proliferation involved in lung morphogenesis / regulation of axon regeneration / mitogen-activated protein kinase kinase / peptidyl-serine autophosphorylation / MAP-kinase scaffold activity / Signaling by MAP2K mutants / positive regulation of cell motility / regulation of Golgi inheritance / peroxisomal membrane ...anthrax lethal factor endopeptidase / epithelial cell proliferation involved in lung morphogenesis / regulation of axon regeneration / mitogen-activated protein kinase kinase / peptidyl-serine autophosphorylation / MAP-kinase scaffold activity / Signaling by MAP2K mutants / positive regulation of cell motility / regulation of Golgi inheritance / peroxisomal membrane / host cell cytosol / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / positive regulation of axonogenesis / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / face development / MAPK1 (ERK2) activation / MAP kinase kinase activity / thyroid gland development / Uptake and function of anthrax toxins / Schwann cell development / ERK1 and ERK2 cascade / protein serine/threonine/tyrosine kinase activity / myelination / protein serine/threonine kinase activator activity / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / PDZ domain binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein serine/threonine kinase activity / cytoplasmic side of plasma membrane / metalloendopeptidase activity / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / metallopeptidase activity / MAPK cascade / Signaling by BRAF and RAF1 fusions / cell-cell junction / late endosome / heart development / toxin activity / scaffold protein binding / protein tyrosine kinase activity / microtubule / early endosome / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / positive regulation of gene expression / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / mitochondrion / proteolysis / zinc ion binding / extracellular region / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pannifer, A.D. / Wong, T.Y. / Schwarzenbacher, R. / Renatus, M. / Petosa, C. / Collier, R.J. / Bienkowska, J. / Lacy, D.B. / Park, S. / Leppla, S.H. ...Pannifer, A.D. / Wong, T.Y. / Schwarzenbacher, R. / Renatus, M. / Petosa, C. / Collier, R.J. / Bienkowska, J. / Lacy, D.B. / Park, S. / Leppla, S.H. / Hanna, P. / Liddington, R.C. | ||||||
![]() | ![]() Title: Crystal structure of the anthrax lethal factor. Authors: Pannifer, A.D. / Wong, T.Y. / Schwarzenbacher, R. / Renatus, M. / Petosa, C. / Bienkowska, J. / Lacy, D.B. / Collier, R.J. / Park, S. / Leppla, S.H. / Hanna, P. / Liddington, R.C. | ||||||
History |
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Remark 400 | COMPOUND THE AUTHORS NOTE THAT THE MAPKK2 16MER PEPTIDE BOUND IN THE ACTIVE SITE OF THE LETHAL ...COMPOUND THE AUTHORS NOTE THAT THE MAPKK2 16MER PEPTIDE BOUND IN THE ACTIVE SITE OF THE LETHAL FACTOR PROTEIN INFERRED FROM THIS STRUCTURE IS NOT IN THE PRODUCTIVE ORIENTATION FOR PROTEOLYSIS. PLEASE REFER TO THE STRUCTURES WITH PDB ID CODES 1PWV AND 1PWW, FOR THE PRODUCTIVE CONFORMATION OF AN OPTIMAL PEPTIDE SUBSTRATE BOUND IN THE LETHAL FACTOR ACTIVE SITE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 159.3 KB | Display | ![]() |
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PDB format | ![]() | 122.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1j7nSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 90356.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MATURE FORM / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1793.247 Da / Num. of mol.: 1 / Fragment: N-terminus / Source method: obtained synthetically Details: This protein was chemically synthesized. It is based on a sequence from Homo sapiens (human). References: GenBank: 13489054, UniProt: P36507*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 8.4 Å3/Da / Density % sol: 86 % |
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Crystal grow | pH: 8 / Details: 1.9M Ammonium sulfate, 0.2M Tris pH 8.0, 2mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 2001 |
Radiation | Monochromator: 0.87 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→50.6 Å / Num. all: 22906 / Num. obs: 22906 / % possible obs: 84.9 % / Redundancy: 3.7 % / Rsym value: 0.103 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 3.9→4 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.631 / % possible all: 88.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1J7N Resolution: 3.9→50.6 Å / Cor.coef. Fo:Fc: 0.886 / SU B: 27.142 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.6 / Stereochemistry target values: maximum likelihood
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 118.741 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→50.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.9→4.001 Å / Total num. of bins used: 20 /
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