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- PDB-1zm2: Structure of ADP-ribosylated eEF2 in complex with catalytic fragm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zm2 | ||||||
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Title | Structure of ADP-ribosylated eEF2 in complex with catalytic fragment of ETA | ||||||
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![]() | BIOSYNTHETIC PROTEIN/TRANSFERASE / elongation factor / toxin / ADP-ribosylation / BIOSYNTHETIC PROTEIN-TRANSFERASE COMPLEX | ||||||
Function / homology | ![]() NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / nucleotidyltransferase activity ...NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / nucleotidyltransferase activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / ribosome binding / protein-folding chaperone binding / toxin activity / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joergensen, R. / Merrill, A.R. / Yates, S.P. / Marquez, V.E. / Schwan, A.L. / Boesen, T. / Andersen, G.R. | ||||||
![]() | ![]() Title: Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Authors: Joergensen, R. / Merrill, A.R. / Yates, S.P. / Marquez, V.E. / Schwan, A.L. / Boesen, T. / Andersen, G.R. | ||||||
History |
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Remark 400 | COMPOUND RESIDUE 699 IS AN ADP-RIBOSYLATED DIPHTHAMIDE WHICH IS COMPOSED OF DDE WITH A LINK TO APR ...COMPOUND RESIDUE 699 IS AN ADP-RIBOSYLATED DIPHTHAMIDE WHICH IS COMPOSED OF DDE WITH A LINK TO APR LIGANDS. THE COMPLETE ADP-RIBOSYLATED DIPHTHAMIDE CAN ONLY BE OBSERVED IN CHAIN E. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 597.7 KB | Display | ![]() |
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PDB format | ![]() | 482.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zm3C ![]() 1zm4C ![]() 1zm9C ![]() 1aerS ![]() 1n0vS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 93549.320 Da / Num. of mol.: 3 / Fragment: eEF2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 22496.010 Da / Num. of mol.: 3 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 151216, UniProt: P11439*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases #3: Chemical | ChemComp-APR / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 6000, MPD, HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 13, 2005 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.952 Å / Relative weight: 1 |
Reflection | Resolution: 3.07→40 Å / Num. all: 76524 / Num. obs: 75835 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.142 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3.07→3.15 Å / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entries 1n0v and 1aer Resolution: 3.07→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.07→30 Å
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Refine LS restraints |
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