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- PDB-3b8h: Structure of the eEF2-ExoA(E546A)-NAD+ complex -

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Basic information

Entry
Database: PDB / ID: 3b8h
TitleStructure of the eEF2-ExoA(E546A)-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 / 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 / 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
DepositionNov 1, 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)349,7789
Polymers347,7886
Non-polymers1,9903
Water10,665592
1
A: Elongation factor 2
B: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5933
Polymers115,9292
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)116,5933
Polymers115,9292
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)116,5933
Polymers115,9292
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)329.440, 68.160, 191.630
Angle α, β, γ (deg.)90.000, 103.280, 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: 22379.939 Da / Num. of mol.: 3 / Fragment: catalytic domain / Mutation: E546A
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 / 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.: 592 / 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: 3.01 Å3/Da / Density % sol: 59.14 %
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: 2.5→25 Å / Num. all: 144251 / Num. obs: 143628 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 38.246 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.79
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 66455 / Num. unique all: 15781 / Num. unique obs: 15781 / % possible all: 99.7

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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 2B82

2b82


Resolution: 2.5→24.992 Å / FOM work R set: 0.838 / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3084 2.15 %Test set chosen from PDB entry 2B82
Rwork0.214 ---
all0.214 144017 --
obs0.214 143513 99.65 %-
Solvent computationBsol: 45.868 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 248.45 Å2 / Biso mean: 66.04 Å2 / Biso min: 2.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.568 Å20 Å2-1.761 Å2
2--2.194 Å20 Å2
3----1.626 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23995 0 132 592 24719
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.6371
X-RAY DIFFRACTIONf_bond_d0.0021
X-RAY DIFFRACTIONf_chiral_restr0.0421
X-RAY DIFFRACTIONf_dihedral_angle_d16.971
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.1171
LS refinement shellResolution: 2.5→2.539 Å / Total num. of bins used: 281
RfactorNum. reflection% reflection
Rfree0.3218 158 -
Rwork0.3055 486 -
obs-6287 99 %
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)
10.0668-0.019-0.08590.1745-0.11310.2938-0.0695-0.12050.06650.12110.12660.0029-0.1027-0.1065-0.05680.5040.08850.08730.40030.08410.191-25.551719.902632.7852
20.0828-0.01740.10170.1334-0.07220.35980.07210.0584-0.056-0.07460.05890.0343-0.0547-0.0696-0.04590.28640.04270.06020.2080.1427-0.1622-16.886910.487820.3128
30.2383-0.01580.0920.2129-0.05290.2087-0.07080.17440.03530.14310.11930.0119-0.16180.0425-0.11360.43620.01540.00520.2320.00670.0959-14.18228.02593.483
40.13470.06210.02280.5213-0.3310.6479-0.07970.0191-0.01470.11760.35630.1762-0.3379-0.4314-0.25110.25040.06460.08080.40660.09260.0978-28.86949.686338.4358
50.6243-0.062-0.1740.6735-0.27250.73690.13120.11410.07920.1650.0403-0.2071-0.4043-0.1738-0.15020.30510.0590.1180.2190.05160.2349-16.27571.941752.4968
6-0.03490.0416-0.04480.30440.02460.2632-0.01960.016-0.0148-0.15370.0029-0.0518-0.1456-0.0275-0.07110.0706-0.196-0.0113-0.08270.0660.0109-8.6474-11.330762.3268
70.5523-0.26280.20150.3568-0.1370.4289-0.0457-0.10820.0397-0.0510.18670.02480.0146-0.1501-0.10030.0767-0.0819-0.01250.11750.04510.1475-15.5063-19.517173.8016
80.2183-0.09730.16570.3731-0.18060.43810.07220.1295-0.0681-0.38970.0303-0.02370.11550.0871-0.03960.3196-0.01510.00910.1290.02590.0301-5.0394-16.929844.4589
90.32080.0588-0.0430.2259-0.02530.0397-0.12060.24930.2713-0.03570.0230.01860.0080.02930.07530.0734-0.0433-0.00090.13970.01580.171818.841-2.300182.4956
100.3291-0.17340.12870.4846-0.15220.07240.0538-0.15320.1256-0.1518-0.03650.15880.1102-0.1072-0.040.0746-0.0717-0.00210.0969-0.02490.18533.389-7.264590.9884
110.25970.2101-0.07580.24750.15220.0640.0220.0774-0.09130.0549-0.03710.0160.0874-0.07730.01940.0713-0.03280.00740.08780.01490.153114.1691-9.929998.9122
120.40610.0798-0.09060.04360.27450.3644-0.07620.0634-0.2490.09510.0805-0.00010.20790.02520.01080.1255-0.0027-0.00610.0827-0.06540.18217.8207-16.573487.3481
130.0572-0.0153-0.04230.57040.29280.78460.056-0.07130.08710.0511-0.0790.1175-0.44720.2950.0310.5652-0.1912-0.00560.3037-0.00380.197625.916253.205128.2067
140.0801-0.05950.295-0.02070.03210.12240.05520.33230.084-0.1292-0.134-0.0581-0.23070.43160.09370.4458-0.11030.01920.4220.1956-0.26731.482440.523516.9955
150.1238-0.06980.08390.1614-0.0005-0.0506-0.00120.1930.0864-0.2535-0.0480.0284-0.23390.34530.04780.8352-0.2883-0.07630.65550.28380.207132.522753.5381-3.652
160.37920.0831-0.01230.24390.18280.123-0.1486-0.09950.138-0.14620.01650.1413-0.21880.12870.10680.2408-0.0965-0.00630.222-0.01760.074922.581344.93936.2974
170.29810.00910.05350.44610.02670.251-0.00470.0631-0.04690.18150.0149-0.16290.0276-0.10510.01140.3366-0.0801-0.03590.3610.02530.31336.618537.844550.8923
180.14980.0920.0240.3528-0.14910.1584-0.05950.03630.1313-0.02290.1520.07850.0252-0.1105-0.06240.0886-0.0753-0.05960.08360.08630.228544.560523.159661.0437
190.6428-0.1577-0.07170.2644-0.08370.1732-0.1382-0.02410.2212-0.02180.18420.147-0.0136-0.0315-0.04760.0734-0.0386-0.03510.10220.07010.191238.56415.732174.3079
200.37340.0315-0.03340.26850.1509-0.0948-0.13330.30940.0277-0.36110.0179-0.06120.09790.0260.03780.3331-0.0933-0.04510.34370.14090.15845.188116.22143.9307
210.28060.15490.1330.33160.01380.1489-0.14810.11110.21-0.10370.05350.0429-0.10610.09730.07020.0819-0.042-0.00710.10380.00510.178773.538632.291381.3535
220.7058-0.04170.31790.3375-0.07720.20710.0374-0.1865-0.0138-0.1579-0.02320.18590.0664-0.0971-0.0570.0849-0.0208-0.04930.05790.00930.21858.009927.801690.1236
230.0122-0.0860.02860.04740.06340.5977-0.01170.0012-0.0499-0.0072-0.00870.15010.13610.02050.00590.0619-0.0368-0.0030.07040.01120.161168.549825.073897.8834
240.1542-0.0178-0.06150.47720.02890.41430.00750.0289-0.06250.00920.17310.06670.19690.0267-0.14260.0981-0.0218-0.05290.0873-0.06920.267271.916318.153586.4077
250.0309-0.0611-0.02780.2029-0.04940.06270.09260.06190.0884-0.2684-0.1883-0.20770.03530.00160.06341.31210.41470.28511.17160.24141.1891-81.6799-13.597932.1615
260.0228-0.00750.01780.0943-0.13430.0711-0.0726-0.0226-0.0046-0.29190.0665-0.0188-0.0469-0.08330.01741.5640.54210.22571.09350.36320.642-73.263-23.179919.7609
27-0.0091-0.0089-0.01420.0782-0.0034-0.0895-0.08080.10440.0611-0.1576-0.0854-0.03940.122-0.15110.13861.58440.0063-0.03761.33510.04830.878-69.9997-5.42013.2284
280.3277-0.20490.0440.31630.05320.27050.32330.1412-0.0277-0.3521-0.04150.0719-0.1921-0.1263-0.11780.98240.41370.0011.01590.04420.7322-84.9749-23.557938.3093
290.34640.0709-0.02770.80760.19310.41460.15870.0013-0.0729-0.2646-0.2999-0.29-0.1941-0.14240.10110.51460.12720.05210.6020.08140.6036-71.9677-31.735851.4709
300.38660.0024-0.02380.1933-0.10870.04010.0720.08540.2403-0.0704-0.0814-0.094-0.05570.04920.05330.09940.00960.01480.13590.14350.2172-64.4206-45.367460.9339
310.530.0074-0.28730.1905-0.1310.3345-0.0081-0.08490.1878-0.099-0.02430.00490.04210.10020.02850.0875-0.0366-0.01520.09970.0480.2065-70.6669-52.971473.1544
320.47060.0019-0.19940.4121-0.0315-0.00570.11890.3180.0859-0.4375-0.087-0.1241-0.0257-0.204-0.1030.39420.19980.1680.45170.1994-0.011-62.9404-52.242442.968
330.21340.01650.30220.24460.01260.4411-0.15890.19310.1578-0.05720.01460.0465-0.06160.33660.0830.0428-0.0532-0.00890.2626-0.00520.1141-35.6818-37.198581.2675
340.14380.05210.06390.104-0.10560.97010.0398-0.11150.1452-0.0131-0.0007-0.05490.0534-0.2051-0.06370.05380.0226-0.02840.0863-0.00110.2701-51.4025-41.325389.5217
350.28340.11010.2130.6030.44840.4588-0.01070.12060.03350.12650.05020.09190.11070.0457-0.02370.0806-0.01120.01730.075-0.00040.1086-41.4005-44.267397.6343
360.55420.2795-0.09050.81250.62430.7256-0.11640.1977-0.05890.11660.10290.09010.21310.1762-0.01990.04650.0466-0.02260.0851-0.08740.09-37.5975-51.320886.3937
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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