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- PDB-4x33: Structure of the Elongator cofactor complex Kti11/Kti13 at 1.45A -

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Basic information

Entry
Database: PDB / ID: 4x33
TitleStructure of the Elongator cofactor complex Kti11/Kti13 at 1.45A
Components
  • Diphthamide biosynthesis protein 3
  • Protein ATS1
KeywordsELECTRON TRANSPORT / Electron transfer / tRNA modification / Complex
Function / homology
Function and homology information


2-(3-amino-3-carboxypropyl)histidine synthase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Synthesis of diphthamide-EEF2 / tRNA wobble uridine modification / iron chaperone activity / protein histidyl modification to diphthamide / ferrous iron binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process ...2-(3-amino-3-carboxypropyl)histidine synthase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Synthesis of diphthamide-EEF2 / tRNA wobble uridine modification / iron chaperone activity / protein histidyl modification to diphthamide / ferrous iron binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / iron ion binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Microbial ribonuclease fold / DPH Zinc finger / DPH-type metal-binding domain / DPH-type metal-binding domain superfamily / CSL zinc finger / DPH-type metal-binding (MB) domain profile. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 ...Microbial ribonuclease fold / DPH Zinc finger / DPH-type metal-binding domain / DPH-type metal-binding domain superfamily / CSL zinc finger / DPH-type metal-binding (MB) domain profile. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Roll / Alpha Beta
Similarity search - Domain/homology
1,2-DIMETHOXYETHANE / : / Protein KTI13 / Diphthamide biosynthesis protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsKolaj-Robin, O. / McEwen, A.G. / Cavarelli, J. / Seraphin, B.
Funding support France, 1items
OrganizationGrant numberCountry
France
CitationJournal: Febs J. / Year: 2015
Title: Structure of the Elongator cofactor complex Kti11/Kti13 provides insight into the role of Kti13 in Elongator-dependent tRNA modification.
Authors: Kolaj-Robin, O. / McEwen, A.G. / Cavarelli, J. / Seraphin, B.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diphthamide biosynthesis protein 3
B: Protein ATS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,43513
Polymers43,9812
Non-polymers45411
Water9,890549
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-80 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.790, 89.009, 163.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-258-

ARG

21A-215-

HOH

31B-595-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Diphthamide biosynthesis protein 3 / Kluyveromyces lactis toxin-insensitive protein 11


Mass: 7458.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: KTI11, DPH3, YBL071W-A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus(DES)-RIL / References: UniProt: Q3E840
#2: Protein Protein ATS1 / Alpha-tubulin suppressor 1


Mass: 36522.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ATS1, YAL020C, FUN28, YAL006 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus(DES)-RIL / References: UniProt: P31386

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Non-polymers , 5 types, 560 molecules

#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DXE / 1,2-DIMETHOXYETHANE


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 22.5% PEG 3350, 0.2 MgCl2 and 0.1M Tris pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.45→44.5 Å / Num. obs: 64706 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.044 / Net I/σ(I): 9.5 / Num. measured all: 431552
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.45-1.476.82.1450.82086330900.2750.87597.3
7.94-44.55.60.04635.625894640.9980.02198.9

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
BUSTER-TNT2.10.1refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→21.23 Å / Cor.coef. Fo:Fc: 0.9728 / Cor.coef. Fo:Fc free: 0.9688 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.063 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 3209 4.97 %RANDOM
Rwork0.1497 ---
obs0.1511 64580 99.81 %-
Displacement parametersBiso max: 123.99 Å2 / Biso mean: 26.12 Å2 / Biso min: 3.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.0225 Å20 Å20 Å2
2--0.3353 Å20 Å2
3----0.3578 Å2
Refine analyzeLuzzati coordinate error obs: 0.169 Å
Refinement stepCycle: final / Resolution: 1.45→21.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 20 571 3587
Biso mean--37.74 39.28 -
Num. residues----385
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1433SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1057HARMONIC5
X-RAY DIFFRACTIONt_it6556HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7602SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6563HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11843HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.27
X-RAY DIFFRACTIONt_other_torsion14.04
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2572 204 4.39 %
Rwork0.231 4445 -
all0.2322 4649 -
obs--99.81 %
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)
12.30191.2047-1.11410.8267-0.19781.4351-0.04380.2276-0.029-0.21590.0957-0.05770.05190.051-0.0519-0.00540.00350.0679-0.01910.04-0.038816.06739.442546.4033
21.5792-0.58680.19341.52750.3211.47870.06710.1491-0.2024-0.26570.01930.26420.1935-0.2325-0.0863-0.0012-0.041-0.0337-0.01120.0189-0.0268-7.634322.366554.963
31.6789-0.030.34822.1389-0.71880.72820.0440.0934-0.1942-0.3380.06980.12570.2727-0.0356-0.11380.0214-0.0113-0.0213-0.07440.0009-0.0363.738913.931157.247
40.5405-0.24350.42521.3932-0.61951.25690.06890.0891-0.0722-0.217-0.0669-0.1140.2520.1846-0.0020.01320.03660.0213-0.03170.0098-0.008816.055113.255761.8866
50.85520.11360.12381.0782-0.64621.54060.04940.0120.0603-0.0149-0.1007-0.1470.06470.23610.0513-0.06170.01480.00160.00260.02770.003522.191124.058467.0487
61.2358-0.5490.13121.3545-0.84971.6062-0.0073-0.02110.13960.1418-0.0514-0.1734-0.09610.1710.0586-0.0183-0.0232-0.008-0.02580.02090.018216.076133.74173.6802
71.28930.1384-0.25370.5863-0.11191.7220.0763-0.12230.13130.0959-0.01970.0215-0.21830.0568-0.05650.0003-0.0040.0168-0.0480.0080.00184.085639.087773.7915
81.32620.2749-0.27280.706-0.18432.20740.0551-0.01350.0564-0.020.00590.1036-0.0275-0.2157-0.061-0.050.00870.0155-0.02120.0335-0.0025-6.802234.526866.3286
91.2487-0.156-0.72220.81490.5731.09480.0035-0.1082-0.00880.03080.07390.06040.2051-0.0085-0.0774-0.0106-0.01270.00160.0140.0338-0.0156-4.280924.702765.6657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|101 }A2 - 101
2X-RAY DIFFRACTION2{ B|2 - B|31 }B2 - 31
3X-RAY DIFFRACTION3{ B|35 - B|88 }B35 - 88
4X-RAY DIFFRACTION4{ B|89 - B|129 }B89 - 129
5X-RAY DIFFRACTION5{ B|130 - B|179 }B130 - 179
6X-RAY DIFFRACTION6{ B|180 - B|219 }B180 - 219
7X-RAY DIFFRACTION7{ B|220 - B|260 }B220 - 260
8X-RAY DIFFRACTION8{ B|261 - B|317 }B261 - 317
9X-RAY DIFFRACTION9{ B|318 - B|333 }B318 - 333

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