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- PDB-3b78: Structure of the eEF2-ExoA(R551H)-NAD+ complex -

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Basic information

Entry
Database: PDB / ID: 3b78
TitleStructure of the eEF2-ExoA(R551H)-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: 2.5 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
DepositionOct 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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)349,8959
Polymers347,9056
Non-polymers1,9903
Water8,971498
1
A: Elongation factor 2
B: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6323
Polymers115,9682
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Elongation factor 2
D: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6323
Polymers115,9682
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Elongation factor 2
F: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6323
Polymers115,9682
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)327.136, 68.128, 190.577
Angle α, β, γ (deg.)90.000, 102.994, 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: 22418.928 Da / Num. of mol.: 3 / Fragment: catalytic domain / Mutation: R551H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: eta / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE ILE->VAL AND GLY->SER SEQUCE CONFLICTS AT RESIDUES 432 AND 540 IN THE UNIPROT DATABASE.

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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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2007
Details: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 144422 / Num. obs: 134457 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.176 / Χ2: 1.045 / Net I/σ(I): 6.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 1.3 / Num. unique all: 10308 / Χ2: 1.027 / % possible all: 72.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.5→46.55 Å / FOM work R set: 0.818 / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2810 2.11 %Test set chosen from eEF2-ExoA(E546H)-NAD+
Rwork0.206 ---
all0.206 142482 --
obs0.206 132950 93.31 %-
Solvent computationBsol: 50.672 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 352 Å2 / Biso mean: 71.95 Å2 / Biso min: 4.13 Å2
Baniso -1Baniso -2Baniso -3
1--3.216 Å20 Å2-0.43 Å2
2--8.636 Å20 Å2
3----5.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23986 0 132 498 24616
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.5911
X-RAY DIFFRACTIONf_bond_d0.0021
X-RAY DIFFRACTIONf_chiral_restr0.0391
X-RAY DIFFRACTIONf_dihedral_angle_d15.1741
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.1241
LS refinement shellResolution: 2.5→2.5431 Å
RfactorNum. reflection% reflection
Rfree0.3568 123 -
Rwork0.2976 --
obs-4833 70 %
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)
10.1493-0.0302-0.00030.5235-0.72061.0890.0102-0.01910.11980.15730.13690.0509-0.4131-0.15-0.12590.44220.05710.08410.39770.06550.2236-25.383820.191332.7188
20.16760.02630.18880.7082-0.57641.22420.07330.0642-0.0376-0.13070.04410.02110.05260.0207-0.10970.24680.00970.05390.17320.02710.0677-16.673210.908120.2468
30.1677-0.03660.15860.6169-0.96591.11810.070.06360.07480.23290.01270.0796-0.098-0.0887-0.09770.28690.0130.03320.20670.00390.1439-14.194728.50473.4865
40.3344-0.1071-0.13960.6248-0.73691.5277-0.0731-0.0679-0.04850.11650.35120.2753-0.3251-0.5869-0.2590.2720.03950.11310.48530.05020.2244-28.5469.911538.2843
50.1103-0.1719-0.01870.3631-0.80981.23060.10750.0282-0.00080.23770.0582-0.1091-0.2638-0.2312-0.1140.31950.05250.030.27810.00120.2803-15.88942.128152.3101
60.1897-0.05030.09360.6569-0.25230.7908-0.0114-0.0166-0.0412-0.19850.0197-0.1631-0.1294-0.0801-0.05420.2029-0.0789-0.01760.09340.03570.1196-8.2779-11.161162.0801
70.2990.01860.39880.5265-0.3330.9189-0.1339-0.23830.0085-0.03450.18860.00750.0536-0.3473-0.17260.0477-0.0766-0.02660.13320.01550.1632-15.1242-19.48873.4712
80.3738-0.1580.14720.8255-0.77731.03910.11630.1952-0.1129-0.41070.01040.02230.30970.2786-0.05650.3034-0.0176-0.00670.1789-0.0040.1224-4.6369-16.597344.2032
90.09250.1247-0.05350.58940.3610.3889-0.08720.32360.2119-0.2836-0.04240.2064-0.132-0.04450.09250.0377-0.1135-0.02260.13360.05920.224419.0431-2.231182.1579
100.60390.0130.82070.1943-0.01840.86630.1382-0.44580.0855-0.1484-0.08620.070.2844-0.5106-0.01770.0006-0.0793-0.00560.1559-0.00760.19883.8025-7.289691.1153
110.10150.14160.13060.60560.39161.007-0.1871-0.1724-0.06160.44230.19180.02310.5398-0.1890.1382-0.23-0.2960.09-0.14660.0930.077314.463-9.888198.5671
120.20430.0082-0.13810.22740.26470.6806-0.0075-0.072-0.21690.06760.15240.12280.43990.0855-0.07260.1279-0.005-0.014-0.03940.01070.16618.2314-16.492686.9283
130.14390.04580.20360.75110.05151.13270.16430.01280.2451-0.0503-0.19940.0508-0.80.44710.01850.6387-0.16720.0470.35330.01620.297326.142753.597528.077
140.32580.03430.46680.2615-0.02010.45890.02230.2461-0.0063-0.1292-0.0756-0.0231-0.22270.50550.06750.4084-0.07380.03150.42050.09270.044431.695140.928916.7869
150.2761-0.03990.720.80810.00250.29040.00660.35240.1303-0.5730.00120.0768-0.04620.50730.03510.7712-0.29590.01980.60450.20320.297432.604654.0301-3.7894
160.59370.19410.21970.41150.25310.5972-0.1012-0.16510.1403-0.1209-0.02430.1438-0.25540.04490.11270.2578-0.06980.02610.2338-0.04250.157722.866345.267236.0553
17-0.1598-0.05670.33780.5347-0.22030.5-0.0754-0.0026-0.02840.2247-0.0013-0.31160.0622-0.0020.05980.2258-0.0416-0.03950.351-0.02170.396436.873938.112950.4273
180.31620.02870.19820.5873-0.42130.6463-0.08670.04680.107-0.01770.0970.0340.0518-0.14-0.02050.0269-0.0317-0.05280.07340.06850.211444.597923.357560.5451
190.3210.01780.08820.06630.03950.2033-0.1992-0.06980.24470.06060.16350.0494-0.0462-0.0815-0.16150.0017-0.0805-0.01420.03210.07670.198138.524815.877573.949
200.4462-0.35630.41450.5404-0.15620.7728-0.00880.4038-0.0533-0.2876-0.0864-0.0620.21160.36250.12750.1996-0.03170.00140.36290.07740.139745.173516.456943.5523
210.61820.41670.05810.4250.16120.1126-0.05940.48870.3508-0.3166-0.0290.0865-0.316-0.0880.053-0.0404-0.1808-0.03410.07420.01010.192873.252432.448880.9436
220.43550.22260.33570.53860.14760.16720.0728-0.2097-0.0787-0.1524-0.0010.11730.0927-0.3402-0.00080.1631-0.0485-0.03580.10340.00670.256757.85627.986589.7283
230.01420.110.07960.49230.70361.2708-0.2369-0.0282-0.15430.4612-0.02310.28150.5769-0.1839-0.0103-0.2588-0.2985-0.0272-0.35610.05370.125868.30125.215797.4651
240.25270.1552-0.09170.25560.24340.6644-0.02640.0048-0.19290.00080.18260.06710.32060.0367-0.08860.13110.0038-0.02480.023-0.02130.231371.744118.242385.978
250.1096-0.1409-0.020.1221-0.11390.22780.160.11040.2016-0.3033-0.2655-0.3212-0.082-0.00060.01381.22990.57830.59941.03320.43781.2886-81.0006-13.178631.9156
260.11180.0723-0.06830.3096-0.37840.3597-0.1673-0.11290.0559-0.49390.1315-0.1673-0.0267-0.07580.01881.52450.72410.40571.09280.31150.5376-72.5593-22.683619.5482
270.0966-0.11170.0470.2531-0.2210.0919-0.06470.17970.0735-0.1203-0.1516-0.1560.1007-0.21160.06191.53240.19710.05651.54320.08770.967-69.4834-4.90993.0449
280.3861-0.00220.22640.2926-0.17620.1510.30470.1040.0774-0.4266-0.07730.1256-0.0249-0.2604-0.03790.75710.48450.07821.152-0.03490.6863-84.1281-23.175637.963
29-0.219-0.12370.11080.3818-0.00550.3830.1114-0.09420.1-0.2702-0.3611-0.445-0.1776-0.34040.08450.54580.14410.07040.79630.02750.8494-71.0509-31.401951.0702
300.4942-0.4730.12820.1912-0.0550.07080.13050.18990.4131-0.1765-0.2693-0.1735-0.0805-0.0205-0.01970.1075-0.0660.02310.13330.21830.321-63.5751-45.086360.564
310.2568-0.0046-0.08490.3027-0.00110.26270.043-0.02680.30370.02690.01770.00170.03920.1162-0.02670.0203-0.0584-0.01010.06340.02120.1792-70.1205-52.865872.5683
320.454-0.1138-0.27051.0635-0.1809-0.1070.29160.66550.0563-1.1572-0.2129-0.0508-0.015-0.1867-0.02160.36850.24140.3550.61680.2823-0.2836-62.1843-51.798442.558
330.06660.50570.41120.44490.27691.0737-0.27350.45690.3989-0.1938-0.00150.1041-0.26340.48320.0544-0.258-0.1698-0.0390.25830.01390.1923-35.0226-37.225580.7896
340.69710.19480.75420.22230.00361.09360.0521-0.18530.2649-0.11490.0407-0.09790.0903-0.3914-0.06650.1359-0.03540.01020.1426-0.01380.2633-50.777-41.162689.0036
350.6510.20830.21110.47070.71891.5682-0.10740.08750.10.0886-0.0260.15140.3797-0.05510.1250.0667-0.00710.01550.0714-0.00710.1565-40.9013-44.262597.1011
360.3030.3612-0.02990.43860.49051.1188-0.1610.1043-0.10590.15160.10540.29690.41890.0981-0.00380.23270.10490.00250.1424-0.04770.2089-36.9897-51.321185.9088
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 2:88AA288
22chain A and resid 89:227AA89227
33chain A and resid 228:310AA228310
44chain A and resid 311:453AA311453
55chain A and resid 454:517AA454517
66chain A and resid 518:612AA518612
77chain A and resid 613:723AA613723
88chain A and resid 724:842AA724842
99chain B and resid 399:455BB399455
1010chain B and resid 456:493BB456493
1111chain B and resid 494:575BB494575
1212chain B and resid 576:605BB576605
1313chain C and resid 2:88CC288
1414chain C and resid 89:227CC89227
1515chain C and resid 228:310CC228310
1616chain C and resid 311:453CC311453
1717chain C and resid 454:517CC454517
1818chain C and resid 518:612CC518612
1919chain C and resid 613:723CC613723
2020chain C and resid 724:842CC724842
2121chain D and resid 399:455DD399455
2222chain D and resid 456:493DD456493
2323chain D and resid 494:575DD494575
2424chain D and resid 576:605DD576605
2525chain E and resid 2:88EE288
2626chain E and resid 89:227EE89227
2727chain E and resid 228:310EE228310
2828chain E and resid 311:453EE311453
2929chain E and resid 454:517EE454517
3030chain E and resid 518:612EE518612
3131chain E and resid 613:723EE613723
3232chain E and resid 724:842EE724842
3333chain F and resid 399:455FF399455
3434chain F and resid 456:493FF456493
3535chain F and resid 494:575FF494575
3636chain F and resid 576:605FF576605

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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