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- PDB-1zm2: Structure of ADP-ribosylated eEF2 in complex with catalytic fragm... -

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Basic information

Entry
Database: PDB / ID: 1zm2
TitleStructure of ADP-ribosylated eEF2 in complex with catalytic fragment of ETA
Components
  • Elongation factor 2EEF2
  • Exotoxin APseudomonas exotoxin
KeywordsBIOSYNTHETIC PROTEIN/TRANSFERASE / elongation factor / toxin / ADP-ribosylation / BIOSYNTHETIC PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


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 / maintenance of translational fidelity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / toxin activity / protein-folding chaperone binding / 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / 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 / Translation factors / EF-G domain III/V-like / Ribosomal Protein S5; domain 2 / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / 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 / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Alpha-Beta Complex / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / : / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 400COMPOUND 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,6957
Polymers348,1366
Non-polymers5591
Water0
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6053
Polymers116,0452
Non-polymers5591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)330.630, 67.840, 191.500
Angle α, β, γ (deg.)90.00, 103.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Elongation factor 2 / EEF2 / EF-2


Mass: 93549.320 Da / Num. of mol.: 3 / Fragment: eEF2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32324
#2: Protein Exotoxin A / Pseudomonas exotoxin / 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) / Gene: eta / Production host: Escherichia coli (E. coli)
References: GenBank: 151216, UniProt: P11439*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2

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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: 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 shellResolution: 3.07→3.15 Å / % possible all: 91

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1n0v and 1aer

1n0v

1aer


Resolution: 3.07→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 1521 thin shells
Rwork0.231 --
all0.232 76524 -
obs0.232 75835 -
Refinement stepCycle: LAST / Resolution: 3.07→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23989 0 35 0 24024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0097
X-RAY DIFFRACTIONc_angle_deg1.45

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