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- PDB-5m2n: Crystal Structure of Elongator subunit Elp2 -

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Basic information

Entry
Database: PDB / ID: 5m2n
TitleCrystal Structure of Elongator subunit Elp2
ComponentsElongator complex protein 2
KeywordsRNA BINDING PROTEIN / Elongator / tRNA modifcation / Elp2 / WD40
Function / homology
Function and homology information


elongator holoenzyme complex / protein urmylation / tRNA wobble uridine modification / protein transport / regulation of translation / microtubule binding / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Elongator complex protein 2 / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Elongator complex protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.812 Å
AuthorsGlatt, S. / Mueller, C.W.
Funding support Germany, Poland, 3items
OrganizationGrant numberCountry
German Research FoundationBR921/9-1 Germany
German Research FoundationMu3173/2-1 Germany
National Science Centre2015/19/B/NZ1/00343 Poland
CitationJournal: EMBO Rep / Year: 2017
Title: Architecture of the yeast Elongator complex.
Authors: Maria I Dauden / Jan Kosinski / Olga Kolaj-Robin / Ambroise Desfosses / Alessandro Ori / Celine Faux / Niklas A Hoffmann / Osita F Onuma / Karin D Breunig / Martin Beck / Carsten Sachse / ...Authors: Maria I Dauden / Jan Kosinski / Olga Kolaj-Robin / Ambroise Desfosses / Alessandro Ori / Celine Faux / Niklas A Hoffmann / Osita F Onuma / Karin D Breunig / Martin Beck / Carsten Sachse / Bertrand Séraphin / Sebastian Glatt / Christoph W Müller /
Abstract: The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is ...The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1-6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub-complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2, and Elp3 subunits form a two-lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.
History
DepositionOct 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongator complex protein 2


Theoretical massNumber of molelcules
Total (without water)90,1291
Polymers90,1291
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.690, 79.690, 532.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Elongator complex protein 2 / Gamma-toxin target 2


Mass: 90129.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ELP2, TOT2, YGR200C, G7725 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: P42935
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris pH 7.5; 10% PEG 6K; 1750 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97898 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 45798 / % possible obs: 99.6 % / Redundancy: 9.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.143 / Net I/σ(I): 14.4
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 2.58 / CC1/2: 0.68 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.812→47.894 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 21.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 2279 4.98 %Random selection
Rwork0.1995 ---
obs0.2014 45798 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.812→47.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 0 0 23 5763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035881
X-RAY DIFFRACTIONf_angle_d0.5577966
X-RAY DIFFRACTIONf_dihedral_angle_d12.5873465
X-RAY DIFFRACTIONf_chiral_restr0.046875
X-RAY DIFFRACTIONf_plane_restr0.0031003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8119-2.87310.34031360.32412594X-RAY DIFFRACTION95
2.8731-2.93990.29561470.27672756X-RAY DIFFRACTION100
2.9399-3.01340.29061410.26632679X-RAY DIFFRACTION100
3.0134-3.09490.26791420.25112730X-RAY DIFFRACTION100
3.0949-3.18590.29651500.25162769X-RAY DIFFRACTION100
3.1859-3.28870.30851360.22522702X-RAY DIFFRACTION100
3.2887-3.40620.26221440.21172701X-RAY DIFFRACTION100
3.4062-3.54260.22231430.20212732X-RAY DIFFRACTION100
3.5426-3.70380.22251420.19272736X-RAY DIFFRACTION100
3.7038-3.89890.23481390.18712732X-RAY DIFFRACTION100
3.8989-4.14310.20661370.17532749X-RAY DIFFRACTION100
4.1431-4.46280.18451430.15052742X-RAY DIFFRACTION100
4.4628-4.91150.17321430.14172711X-RAY DIFFRACTION100
4.9115-5.62120.2171450.16642737X-RAY DIFFRACTION100
5.6212-7.07850.23041480.19772715X-RAY DIFFRACTION100
7.0785-47.90050.2491430.20942735X-RAY DIFFRACTION100
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)
11.01421.1914-0.25644.9621-0.68631.5501-0.07330.0322-0.0043-0.13390.02980.2210.1816-0.20.03180.16620.0259-00.2428-0.00840.214716.697954.5537237.9629
26.82340.8146-0.39262.0118-0.13951.4123-0.13160.0755-0.35970.03990.0631-0.1110.38480.09050.01390.47710.0721-0.01090.21210.020.252930.916337.7772238.3973
30.96890.16640.15464.20560.65841.80940.08490.0135-0.08970.0104-0.0877-0.3940.12150.3809-0.01590.12260.0583-0.01530.29930.04950.285134.793872.6398241.773
42.0261-0.1509-0.26871.74160.60821.98650.0756-0.00930.15690.061-0.05450.0141-0.23130.1255-0.02590.2610.0206-0.00110.18130.04180.192721.906190.6546252.2966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 172 )
2X-RAY DIFFRACTION2chain 'A' and (resid 173 through 324 )
3X-RAY DIFFRACTION3chain 'A' and (resid 325 through 460 )
4X-RAY DIFFRACTION4chain 'A' and (resid 461 through 788 )

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