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- PDB-2zit: Structure of the eEF2-ExoA-NAD+ complex -

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Basic information

Entry
Database: PDB / ID: 2zit
TitleStructure of the eEF2-ExoA-NAD+ complex
Components
  • Elongation factor 2EEF2
  • Exotoxin APseudomonas exotoxin
KeywordsBIOSYNTHETIC PROTEIN/TRANSFERASE / elongation factor / toxin / ADP-ribosylation / toxin-substrate complex / Cytoplasm / GTP-binding / Nucleotide-binding / Phosphoprotein / Protein biosynthesis / RNA-binding / rRNA-binding / Glycosyltransferase / NAD / Transferase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Exotoxin A / Elongation factor 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsJorgensen, R. / Merrill, A.R.
CitationJournal: Embo Rep. / Year: 2008
Title: The nature and character of the transition state for the ADP-ribosyltransferase reaction.
Authors: Jorgensen, R. / Wang, Y. / Visschedyk, D. / Merrill, A.R.
History
DepositionFeb 24, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Apr 3, 2024Group: 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)349,9529
Polymers347,9626
Non-polymers1,9903
Water0
1
A: Elongation factor 2
B: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6513
Polymers115,9872
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Elongation factor 2
D: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6513
Polymers115,9872
Non-polymers6631
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)116,6513
Polymers115,9872
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)326.920, 69.241, 190.483
Angle α, β, γ (deg.)90.000, 103.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Elongation factor 2 / EEF2 / EF-2 / Translation elongation factor 2 / Eukaryotic elongation factor 2 / eEF2 / Ribosomal translocase


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 / Pseudomonas exotoxin / NAD-dependent ADP-ribosyltransferase


Mass: 22437.975 Da / Num. of mol.: 3 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ToxA / Plasmid: pPH1 / Production host: Escherichia coli (E. coli) / Strain (production host): bb101
References: UniProt: P11439, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
Sequence detailsTHIS SEQUENCE IS BASED ON UNIPROT DATABASE, P11439, REF. 1.

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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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 7% PEG-10000, 3.5mM MPD, 100mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 24, 2008
Details: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)
RadiationMonochromator: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 85409 / Num. obs: 84042 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.164 / Χ2: 1.317 / Net I/σ(I): 4.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.4 / Num. unique all: 7292 / Χ2: 0.823 / % possible all: 86.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementStarting model: eEF2-ExoA(E546H)-NAD+

Resolution: 3→19.899 Å / FOM work R set: 0.777 / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml
Details: When refining TLS, the output PDB file always has the ANISOU records for the atoms involved in TLS groups. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_ ...Details: When refining TLS, the output PDB file always has the ANISOU records for the atoms involved in TLS groups. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_individual). The isotropic equivalent B-factor in ATOM records is the mean of the trace of the ANISOU matrix divided by 10000 and multiplied by 8*pi^2 and represents the isotropic equivalent of the total B-factor (B_tls + B_individual). To obtain the individual B-factors, one needs to compute the TLS component (B_tls) using the TLS records in the PDB file header and then subtract it from the total B-factors (on the ANISOU records).
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1662 2.02 %Test set chosen from eEF2-ExoA(E546H)-NAD+
Rwork0.22 ---
all0.22 83683 --
obs0.22 82428 98.5 %-
Solvent computationBsol: 23.395 Å2 / ksol: 0.257 e/Å3
Displacement parametersBiso max: 458.74 Å2 / Biso mean: 95.47 Å2 / Biso min: 3.69 Å2
Baniso -1Baniso -2Baniso -3
1--10.702 Å20 Å26.592 Å2
2--15.735 Å20 Å2
3----6.866 Å2
Refinement stepCycle: LAST / Resolution: 3→19.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23989 0 132 0 24121
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.561
X-RAY DIFFRACTIONf_bond_d0.0021
X-RAY DIFFRACTIONf_chiral_restr0.0351
X-RAY DIFFRACTIONf_dihedral_angle_d15.3261
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.1231
LS refinement shellResolution: 3→3.09 Å / Total num. of bins used: 162
RfactorNum. reflection% reflection
Rfree0.345 135 -
Rwork0.298 421 -
obs-5928 88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04390.07110.55880.7446-0.23210.35010.1057-0.37060.1355-0.0460.0654-0.0958-0.1941-0.6598-0.14690.67250.07410.16491.17040.26210.4554-25.550520.001832.3274
2-0.05970.00080.31290.3433-0.34031.10140.07390.1384-0.32180.05740.20630.03230.023-0.4093-0.07330.3582-0.05370.22760.67840.3692-0.0995-16.879610.496520.0614
30.2344-0.06170.18850.5194-0.75560.2085-0.13860.1559-0.06060.08550.31080.15580.1021-0.1591-0.09720.46750.0350.11820.83720.09460.2395-14.131328.20293.3948
40.90840.2092-0.34341.1206-1.19281.2241-0.0658-0.20760.02380.39090.60080.4128-0.5256-0.8271-0.49120.5743-0.00220.2081.20320.220.2907-28.91329.846838.1028
50.7923-0.3675-0.08131.5249-0.81951.1623-0.0160.09360.30910.3180.1633-0.19070.0587-0.5942-0.10570.67540.0440.14930.66830.01880.3473-16.21531.958151.9981
60.1181-0.57030.07340.74010.07381.1480.1042-0.0280.0568-0.17540.0194-0.1535-0.4453-0.0349-0.06870.2655-0.1758-0.02930.09630.02660.0934-8.6528-11.438161.7736
70.6693-0.09180.1470.369-0.42091.4529-0.4412-0.44830.09430.78590.88170.4778-0.2395-0.98470.0331-0.7857-0.6607-0.4296-0.2812-0.1994-0.1007-15.5072-19.578173.2621
81.173-0.3318-0.23451.5105-0.9421-0.21360.12890.68660.0152-0.79050.02220.00870.38760.3096-0.10830.5384-0.0870.07050.38510.0860.0955-4.9898-17.071844.0496
91.72330.22250.61280.62870.01740.199-0.07830.69270.2833-0.0073-0.0403-0.153-0.18940.31530.14350.0986-0.1268-0.01620.1646-0.02540.169818.5904-2.13181.7349
100.61540.35070.7310.40880.18011.55990.1341-0.3260.35150.01220.02110.14190.1157-0.63660.03260.1199-0.09580.02340.2274-0.08990.2753.249-7.065890.5341
11-0.0295-0.5188-0.0090.08540.48680.8124-0.0910.0366-0.26230.15310.05740.26870.3934-0.2070.11690.1589-0.09170.03920.08490.00460.216813.7338-9.599598.1735
120.781-0.34020.30970.45280.33880.4875-0.19180.0482-0.63760.15350.13830.12720.32660.1773-0.08620.0566-0.12340.01150.0186-0.15820.36517.5649-16.373786.797
130.073-0.03780.15150.8863-0.60760.86870.153-0.01330.24-0.226-0.2464-0.125-0.36570.33030.04850.6105-0.2240.14870.49630.10710.360425.812653.777228.0154
140.4268-0.02320.89510.1723-0.05520.42230.01580.63690.0865-0.0641-0.0981-0.1711-0.08180.67740.0860.4773-0.05660.08020.84940.17240.050931.254641.051916.9076
150.3583-0.010.91550.3549-0.28790.4294-0.27280.65070.2677-0.23180.14820.02320.31430.72640.14190.9671-0.27540.09331.30220.36510.42132.245654.0484-3.7386
161.390.2963-0.15650.4286-0.07370.1055-0.1109-0.17690.1175-0.0980.06270.0922-0.12660.11640.04010.3598-0.1680.04070.54660.02150.216822.53345.563436.1331
171.7751-1.03290.68270.6575-0.22620.20770.043-0.32730.19170.0696-0.1071-0.2610.4522-0.22870.09750.4127-0.19680.12280.6676-0.04190.30436.646538.207650.6777
180.50350.1284-0.56490.8325-0.68221.24290.02590.28780.413-0.02810.40660.091-0.019-0.3604-0.15830.0961-0.1698-0.06290.12350.34140.265844.412223.332260.6344
190.64760.3834-0.28040.442-0.25010.52-0.3054-0.07310.65090.15810.41150.1772-0.1492-0.4853-0.1045-0.3662-0.5581-0.0486-0.33890.17440.294338.388615.88573.6756
201.3137-0.25140.1611.8421-0.1115-1.9023-0.2230.91580.0102-1.13770.2087-0.0610.51020.10970.06010.7573-0.3902-0.0710.84820.2760.167645.202816.467243.5591
212.07160.4365-0.08160.9014-0.20450.30160.09670.62210.4032-0.0643-0.0606-0.2504-0.36710.12070.00890.0754-0.0998-0.0030.0067-0.05290.174972.925432.870180.7621
220.00640.17870.0337-0.0451-0.80750.93940.1479-0.3002-0.23860.09890.31710.666-0.2677-0.4636-0.16810.1711-0.0544-0.062-0.16790.03760.375257.470928.2789.4644
230.2205-0.1026-0.16761.40140.13840.1013-0.41790.0300.30560.35890.10210.1171-0.31130.14250.0889-0.14870.0664-0.4830.14240.24467.843425.644897.2652
240.3204-0.24260.08020.3885-0.01420.3763-0.0769-0.1042-0.2045-0.01750.24810.16490.23280.1711-0.14750.1213-0.0592-0.02850.0031-0.12860.433871.515418.687785.9182
253.0257-0.3574-0.17891.0125-0.16420.92190.3313-0.25290.306-0.634-0.6718-0.7549-0.01270.00250.17581.29140.42010.60581.55370.53711.5328-80.964-14.256631.9703
260.08840.08090.2630.3513-1.02090.8320.1050.33990.2911-0.38050.2238-0.21290.124-0.0674-0.23032.00680.42580.55121.6140.40440.9773-72.3696-23.820719.693
270.1624-0.0168-0.49230.4253-0.23410.7598-0.50330.06560.06450.28520.37240.17790.42830.13010.08471.9628-0.05760.0881.98250.22571.5511-69.0682-6.08423.3231
280.51190.17810.20951.1503-1.02110.63680.0530.08250.2653-0.30670.42860.09040.024-0.4367-0.27951.25890.24630.241.64740.0811.1395-84.2363-24.128838.1271
291.0402-0.4928-0.11721.4982-0.631.10760.44120.06180.3099-0.4549-0.464-0.53220.1215-0.40310.090.98450.08090.16411.23280.11740.9589-71.3446-32.341851.2265
300.6088-0.71680.35270.6033-0.44140.39890.13010.26180.5393-0.1168-0.3232-0.2198-0.1169-0.08740.00970.238-0.0284-0.01940.21860.30150.3595-63.9089-46.005360.6597
310.55870.24810.13650.2840.0790.06980.0056-0.07980.5046-0.1078-0.08820.05990.0435-0.129-0.08680.0454-0.11-0.07770.05190.12810.2054-70.3228-53.780972.5393
321.0352-0.0539-0.92961.6081-0.8695-0.570.02961.10910.2243-1.2865-0.063-0.36470.536-0.2544-0.04150.99120.20550.23661.08670.32730.1678-62.3555-53.080442.6581
331.101-0.1960.39110.564-0.01980.4768-0.2070.60640.6556-0.20010.1245-0.2714-0.1450.45570.05390.0421-0.1723-0.02360.23960.00250.1122-35.5975-37.30380.6954
340.49940.28461.16670.41630.00131.82330.0641-0.1180.0778-0.13950.19550.0535-0.0719-0.5493-0.24370.0807-0.03280.01590.14430.04530.3583-51.2105-41.602488.9895
351.2871-0.0929-0.37361.63090.36520.9768-0.26870.1496-0.02680.19830.43330.34070.1812-0.0666-0.03460.0747-0.00130.05040.09070.03410.1694-41.2527-44.427397.0844
360.32240.4791-0.3420.7571.01481.7552-0.14770.0769-0.1130.16350.0730.21580.46070.18820.0780.18590.06880.00170.17940.0110.316-37.2605-51.4485.8794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A resid 2:88A0
2X-RAY DIFFRACTION2chain A resid 89:227A0
3X-RAY DIFFRACTION3chain A resid 228:310A0
4X-RAY DIFFRACTION4chain A resid 311:453A0
5X-RAY DIFFRACTION5chain A resid 454:517A0
6X-RAY DIFFRACTION6chain A resid 518:612A0
7X-RAY DIFFRACTION7chain A resid 613:723A0
8X-RAY DIFFRACTION8chain A resid 724:842A0
9X-RAY DIFFRACTION9chain B resid 399:455B0
10X-RAY DIFFRACTION10chain B resid 456:493B0
11X-RAY DIFFRACTION11chain B resid 494:575B0
12X-RAY DIFFRACTION12chain B resid 576:605B0
13X-RAY DIFFRACTION13chain C resid 2:88C0
14X-RAY DIFFRACTION14chain C resid 89:227C0
15X-RAY DIFFRACTION15chain C resid 228:310C0
16X-RAY DIFFRACTION16chain C resid 311:453C0
17X-RAY DIFFRACTION17chain C resid 454:517C0
18X-RAY DIFFRACTION18chain C resid 518:612C0
19X-RAY DIFFRACTION19chain C resid 613:723C0
20X-RAY DIFFRACTION20chain C resid 724:842C0
21X-RAY DIFFRACTION21chain D resid 399:455D0
22X-RAY DIFFRACTION22chain D resid 456:493D0
23X-RAY DIFFRACTION23chain D resid 494:575D0
24X-RAY DIFFRACTION24chain D resid 576:605D0
25X-RAY DIFFRACTION25chain E resid 2:88E0
26X-RAY DIFFRACTION26chain E resid 89:227E0
27X-RAY DIFFRACTION27chain E resid 228:310E0
28X-RAY DIFFRACTION28chain E resid 311:453E0
29X-RAY DIFFRACTION29chain E resid 454:517E0
30X-RAY DIFFRACTION30chain E resid 518:612E0
31X-RAY DIFFRACTION31chain E resid 613:723E0
32X-RAY DIFFRACTION32chain E resid 724:842E0
33X-RAY DIFFRACTION33chain F resid 399:455F0
34X-RAY DIFFRACTION34chain F resid 456:493F0
35X-RAY DIFFRACTION35chain F resid 494:575F0
36X-RAY DIFFRACTION36chain F resid 576:605F0

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