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- PDB-1zm3: Structure of the apo eEF2-ETA complex -

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Basic information

Entry
Database: PDB / ID: 1zm3
TitleStructure of the apo eEF2-ETA complex
Components
  • Elongation factor 2
  • exotoxin A
KeywordsBIOSYNTHETIC PROTEIN/TRANSFERASE / elongation factor / toxin / ADP-ribosylation / BIOSYNTHETIC PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


symbiont-mediated suppression of host translation elongation / NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / symbiont-mediated killing of host cell / Protein methylation / translational elongation / translation elongation factor activity ...symbiont-mediated suppression of host translation elongation / NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / symbiont-mediated killing of host cell / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / nucleotidyltransferase activity / maintenance of translational fidelity / protein-folding chaperone binding / ribosome binding / toxin activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / identical protein binding / cytosol
Similarity search - Function
Yeast translation eEF2 (G' domain) / Yeast translation eEF2 (G' domain) / Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 ...Yeast translation eEF2 (G' domain) / Yeast translation eEF2 (G' domain) / Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Ribosomal Protein S5; domain 2 - #10 / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation factors / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal Protein S5; domain 2 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Concanavalin A-like lectin/glucanase domain superfamily / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Alpha-Beta Complex / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Exotoxin A / Elongation factor 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsJoergensen, R. / Merrill, A.R. / Yates, S.P. / Marquez, V.E. / Schwan, A.L. / Boesen, T. / Andersen, G.R.
CitationJournal: Nature / Year: 2005
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
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 2
B: exotoxin A
C: Elongation factor 2
D: exotoxin A
E: Elongation factor 2
F: exotoxin A


Theoretical massNumber of molelcules
Total (without water)348,1366
Polymers348,1366
Non-polymers00
Water00
1
A: Elongation factor 2
B: exotoxin A


Theoretical massNumber of molelcules
Total (without water)116,0452
Polymers116,0452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Elongation factor 2
D: exotoxin A


Theoretical massNumber of molelcules
Total (without water)116,0452
Polymers116,0452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Elongation factor 2
F: exotoxin A


Theoretical massNumber of molelcules
Total (without water)116,0452
Polymers116,0452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)329.430, 69.090, 190.800
Angle α, β, γ (deg.)90.00, 103.46, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is one molecule of eEF2 in complex with one molecule of ETA

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Components

#1: Protein Elongation factor 2 / EF-2


Mass: 93549.320 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32324
#2: Protein exotoxin A / NAD-DEPENDENT ADP-RIBOSYLTRANSFERASE


Mass: 22496.010 Da / Num. of mol.: 3 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
References: GenBank: 151216, UniProt: P11439*PLUS, NAD+-diphthamide ADP-ribosyltransferase

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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: 2.7 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 6000, MPD, HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.952 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 13, 2005
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.952 Å / Relative weight: 1
ReflectionResolution: 3.07→40 Å / Num. all: 78770 / Num. obs: 77195 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.093 / Net I/σ(I): 16.5
Reflection shellResolution: 3.07→3.15 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.41 / % possible all: 90

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1n0u and 1aer

1n0u

1aer


Resolution: 3.07→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: A699, C699 and E699 are MODELLED AS His, since diphthamide modification was disordered.
RfactorNum. reflectionSelection details
Rfree0.282 1536 thin shells
Rwork0.249 --
all0.25 78770 -
obs0.25 77195 -
Refinement stepCycle: LAST / Resolution: 3.07→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23979 0 0 0 23979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0118
X-RAY DIFFRACTIONc_angle_deg1.55

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