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- PDB-3b82: Structure of the eEF2-ExoA(E546H)-NAD+ complex -

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Basic information

Entry
Database: PDB / ID: 3b82
TitleStructure of the eEF2-ExoA(E546H)-NAD+ complex
Components
  • Elongation factor 2
  • Exotoxin A
KeywordsBIOSYNTHETIC PROTEIN/TRANSFERASE / elongation factor / toxin / ADP-ribosylation / toxin-substrate complex / Cytoplasm / GTP-binding / Nucleotide-binding / Phosphorylation / 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 / ribosome binding / protein-folding chaperone 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 / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / 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
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: 2.35 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 31, 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 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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)349,9799
Polymers347,9896
Non-polymers1,9903
Water9,872548
1
A: Elongation factor 2
B: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6603
Polymers115,9962
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)116,6603
Polymers115,9962
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)116,6603
Polymers115,9962
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)327.570, 68.460, 189.990
Angle α, β, γ (deg.)90.000, 103.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Elongation factor 2 / 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 / NAD-dependent ADP-ribosyltransferase


Mass: 22447.008 Da / Num. of mol.: 3 / Fragment: catalytic domain / Mutation: E546H
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, NAD+-diphthamide ADP-ribosyltransferase
#3: Chemical ChemComp-NAD / 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


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
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: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2006 / Details: Si(111) double-crystal monochromator
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. all: 171813 / Num. obs: 169084 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 39.284 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9.07
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.6 / Num. measured obs: 23346 / Num. unique all: 10376 / Num. unique obs: 8495 / % possible all: 81.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementStarting model: PDB entry 1ZM9

1zm9


Resolution: 2.35→25 Å / FOM work R set: 0.815 / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3701 2.19 %Test set chosen from 1ZM9 and extended to 2.35A
Rwork0.215 ---
all0.215 171592 --
obs0.215 169070 98.53 %-
Solvent computationBsol: 43.606 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 317.73 Å2 / Biso mean: 71.47 Å2 / Biso min: 7.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.484 Å20 Å2-2.325 Å2
2--4.304 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24002 0 132 548 24682
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.5471
X-RAY DIFFRACTIONf_bond_d0.0021
X-RAY DIFFRACTIONf_chiral_restr0.0361
X-RAY DIFFRACTIONf_dihedral_angle_d14.7251
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.1191
LS refinement shellResolution: 2.35→2.38 Å / Total num. of bins used: 331
RfactorNum. reflection% reflection
Rfree0.4104 120 -
Rwork0.3672 63 -
obs-4826 76 %
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)
10.3494-0.0619-0.32020.56270.0801-0.7267-0.1037-0.08470.08880.20320.1729-0.0015-0.2487-0.2074-0.05690.54980.09820.03410.55120.13680.1802-25.409720.047232.5296
20.11360.03010.19640.3682-0.19420.9070.0694-0.0055-0.062-0.10870.0983-0.03180.1005-0.0532-0.09040.33360.00620.01420.27990.133-0.0778-16.723810.787920.0911
30.4356-0.14280.1460.768-0.6694-0.054-0.04730.18960.04110.11840.0728-0.01030.0543-0.043-0.03910.34420.0010.01090.20860.0290.0645-14.195628.47943.4494
40.37380.3526-0.20320.9776-0.50090.7021-0.08940.01090.04370.16960.40150.3084-0.3261-0.4967-0.24320.26280.05410.08410.42480.13190.0813-28.6119.786338.0899
50.87820.369-0.32691.0586-0.86750.70580.23660.10920.08470.4875-0.0325-0.2213-0.2799-0.0879-0.1150.33820.02310.00640.17520.04940.1864-15.94152.058152.026
60.38950.18210.35850.6266-0.16770.8987-0.0789-0.13130.0261-0.16070.0005-0.0087-0.1726-0.12680.07080.1845-0.0599-0.02540.04750.00760.0736-8.2205-11.191261.7733
70.3368-0.20190.71490.632-0.47411.109-0.1748-0.1212-0.0073-0.06340.18010.0607-0.0094-0.3378-0.06740.0508-0.0419-0.01650.14970.01190.1602-15.0542-19.525273.169
80.6201-0.32450.49191.0589-0.85520.35530.06870.1827-0.0752-0.50970.04950.02530.26550.2336-0.08850.4029-0.05650.0010.18750.02130.0729-4.5875-16.700443.9671
90.28780.29810.2040.63270.12950.1699-0.05340.19240.2368-0.0735-0.02550.1648-0.00820.04450.06740.0723-0.0618-0.01020.12260.02370.197819.0674-2.159481.8504
101.06950.11710.64220.17490.16930.42450.0795-0.2545-0.0375-0.0644-0.07270.11540.1791-0.2058-0.00330.0803-0.0506-0.0250.1398-0.00680.2293.8692-7.210190.75
110.31930.1742-0.33440.2841-0.04940.3281-0.02070.0538-0.03430.08580.06220.06870.0341-0.1796-0.02990.0962-0.0380.01180.07510.03090.197414.3829-9.822298.2039
120.4355-0.1448-0.03770.30630.08970.4671-0.06180.0452-0.22460.03080.12010.05450.25560.0313-0.12430.1064-0.0027-0.03370.0327-0.04650.211518.1298-16.430986.7504
130.2409-0.114-0.42260.73570.32421.45140.1854-0.15430.1244-0.1205-0.03420.0441-0.62850.4339-0.16020.5989-0.1735-0.02730.328-0.00370.215626.243253.777127.9591
140.0968-0.01580.3216-0.0147-0.03130.80690.0030.34410.0301-0.1633-0.1099-0.0389-0.09110.44350.07790.3789-0.0409-0.01540.40250.2076-0.350131.672941.058416.7415
150.73870.13070.81910.8150.3870.1277-0.14830.47650.0598-0.64880.11520.1244-0.13730.7230.03460.7159-0.25780.01390.56160.21560.064632.654954.0708-3.8048
161.09830.5347-0.39280.481-0.11820.7297-0.0854-0.11680.1553-0.08510.04520.1498-0.27390.06740.05690.2872-0.0854-0.01020.2793-0.01180.112322.938845.467835.9922
170.381-0.5624-0.09851.7039-0.2120.3649-0.0386-0.12050.19190.45530.0335-0.5115-0.0213-0.20790.06110.3785-0.0301-0.10290.3009-0.0640.360136.93738.262750.3376
180.52090.2890.17890.6343-0.6831.1365-0.06880.06810.2218-0.05770.12420.08720.0965-0.1747-0.0640.0362-0.003-0.03590.06670.08350.304444.72623.431260.3656
191.0881-0.06710.14190.362-0.16320.3266-0.1069-0.06290.1171-0.08920.15510.09950.0109-0.104-0.07510.0434-0.0231-0.02780.05120.06990.232738.671315.912973.683
200.7003-0.11560.01850.9250.0849-0.6095-0.07590.40270.0064-0.4383-0.0097-0.03860.13530.17050.07030.2755-0.0682-0.01920.30220.10860.10445.332316.549643.3742
210.26420.45380.270.83090.0930.3345-0.18180.17980.1632-0.12170.07120.0856-0.19540.06540.08070.1258-0.0654-0.02510.1603-0.00440.241173.460732.54980.6381
220.71380.18340.52120.5860.02740.53860.003-0.11350.0389-0.1838-0.02660.01910.0645-0.06840.02860.1321-0.0073-0.03050.0637-0.00510.314758.047328.063589.4495
230.0102-0.0945-0.01540.27280.12120.2208-0.0580.03420.04580.05710.03750.2150.0718-0.11990.02610.0911-0.0395-0.00520.060.01610.177268.515125.300897.1637
240.1803-0.00430.06670.60280.08490.5302-0.00390.0614-0.2474-0.02870.18180.01750.17890.0461-0.18080.08250.00040.00250.0805-0.09390.344471.959318.397485.7575
250.7817-0.66520.11770.6463-0.0182-0.01470.14530.06610.1985-0.3243-0.1231-0.25320.0493-0.0176-0.00281.38750.46910.36641.27880.32591.3312-80.8543-13.606331.8418
260.39210.0580.16520.4893-0.66860.3017-0.2943-0.2381-0.0496-0.13340.3175-0.0272-0.3174-0.17070.03561.62060.54720.25531.27150.36930.8726-72.5192-23.076119.4755
270.3954-0.0394-0.1880.1618-0.0597-0.192-0.31820.24070.10360.22760.2023-0.02110.2650.19360.08571.72190.1105-0.08611.47380.05671.1892-69.2725-5.22693.1776
280.8147-0.39920.22930.6018-0.33680.1570.2910.11390.0312-0.14830.07180.09140.0032-0.0719-0.1690.76010.3681-0.02320.79550.04780.6894-84.0259-23.58537.8586
290.94790.2950.93711.92380.51191.12490.2394-0.2294-0.1774-0.1638-0.3261-0.4756-0.2346-0.27590.08060.53930.0727-0.01980.74860.15510.7041-71.0205-31.807250.7984
301.13010.06660.1830.3817-0.47160.5417-0.05810.17790.4525-0.1066-0.174-0.1397-0.06550.04530.11970.1044-0.0027-0.00060.10550.18880.309-63.5282-45.449460.206
310.83560.1735-0.08860.17430.01470.1345-0.0155-0.09270.3377-0.03740.00360.0983-0.00550.0622-0.00640.0911-0.0508-0.02350.11360.05970.2612-69.931-53.092972.4332
321.52320.2024-0.72031.2215-0.8527-0.19370.02940.79160.219-0.7609-0.0465-0.14560.4228-0.1561-0.0760.46340.14410.2070.60730.25950.0369-62.0967-52.325142.2405
33-0.44650.21330.50470.85830.3171.173-0.23040.21150.1548-0.04180.12170.1185-0.12470.34060.0820.0818-0.0509-0.00970.29450.02520.199-35.0584-37.260680.5131
340.34620.52410.52440.26390.08151.7699-0.0521-0.10080.3062-0.0179-0.1038-0.01970.0903-0.280.10150.03710.0073-0.01650.0646-0.00040.3082-50.7636-41.31788.6753
350.46150.2856-0.20990.3070.07780.627-0.05690.10.07250.0420.04260.12830.1155-0.0270.02110.0736-0.02430.03220.10160.03680.1411-40.8731-44.337696.8027
360.17250.3322-0.32230.06820.17740.8792-0.06460.1604-0.17140.03990.08220.16950.19820.14610.00420.04820.0703-0.00040.0869-0.0580.176-36.9469-51.342385.683
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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