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- PDB-5oa9: Human translation re-initiation complex containing eIF2D -

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Basic information

Entry
Database: PDB / ID: 5oa9
TitleHuman translation re-initiation complex containing eIF2D
ComponentsEukaryotic translation initiation factor 2D
KeywordsTRANSLATION / translation re-initiation complex / translation initiation factor / RNA binding protein / small ribosomal subunit
Function / homology
Function and homology information


IRES-dependent viral translational initiation / ribosome disassembly / formation of translation preinitiation complex / translation initiation factor activity / intracellular protein transport / signaling receptor activity / nuclear body / RNA binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 2D, SUI1 domain / : / : / Eukaryotic translation initiation factor 2D / Pre-PUA domain / Pre-PUA-like domain / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain ...Eukaryotic translation initiation factor 2D, SUI1 domain / : / : / Eukaryotic translation initiation factor 2D / Pre-PUA domain / Pre-PUA-like domain / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / PUA-like superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWeisser, M. / Schaefer, T. / Leibundgut, M. / Boehringer, D. / Aylett, C.H.S. / Ban, N.
CitationJournal: Mol Cell / Year: 2017
Title: Structural and Functional Insights into Human Re-initiation Complexes.
Authors: Melanie Weisser / Tanja Schäfer / Marc Leibundgut / Daniel Böhringer / Christopher Herbert Stanley Aylett / Nenad Ban /
Abstract: After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large ...After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which are important in cancer. Key ribosomal binding proteins involved in re-initiation are the eukaryotic translation initiation factor 2D (eIF2D) or the homologous complex of MCT-1/DENR. We determined the structures of these factors bound to the human 40S ribosomal subunit in complex with initiator tRNA positioned on an mRNA start codon in the P-site using a combination of cryoelectron microscopy and X-ray crystallography. The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA.
History
DepositionJun 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 2D


Theoretical massNumber of molelcules
Total (without water)23,2771
Polymers23,2771
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.720, 50.720, 197.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Eukaryotic translation initiation factor 2D / eIF2d / Hepatocellular carcinoma-associated antigen 56 / Ligatin


Mass: 23277.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2D, HCA56, LGTN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus pRIL / References: UniProt: P41214
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 1:1 mix protein (50 mM HEPES-KOH pH 7.6, 150 mM KCl, 1 mM TCEP) with reservoir solution (100 mM HEPES-KOH pH 7.6, 25 mM sodium formate, 25 mM ammonium acetate, 25 mM sodium citrate tribasic, ...Details: 1:1 mix protein (50 mM HEPES-KOH pH 7.6, 150 mM KCl, 1 mM TCEP) with reservoir solution (100 mM HEPES-KOH pH 7.6, 25 mM sodium formate, 25 mM ammonium acetate, 25 mM sodium citrate tribasic, 25 mM sodium potassium tartrate, 10.7% PEG3350, 10.7% MPD, 10.7% PEG1000)

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.35 Å / Num. obs: 24936 / % possible obs: 99.85 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 1.026 / CC1/2: 0.71 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→24.67 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1908 7.89 %
Rwork0.19 --
obs0.193 24173 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 0 134 1738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051633
X-RAY DIFFRACTIONf_angle_d0.8292215
X-RAY DIFFRACTIONf_dihedral_angle_d13.617629
X-RAY DIFFRACTIONf_chiral_restr0.034258
X-RAY DIFFRACTIONf_plane_restr0.004285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84510.30891170.30041408X-RAY DIFFRACTION88
1.8451-1.8950.33631290.27151439X-RAY DIFFRACTION90
1.895-1.95070.26241270.23841491X-RAY DIFFRACTION92
1.9507-2.01360.31681260.23421525X-RAY DIFFRACTION96
2.0136-2.08560.28341340.21661559X-RAY DIFFRACTION97
2.0856-2.1690.23941340.20951573X-RAY DIFFRACTION97
2.169-2.26770.26261370.2191575X-RAY DIFFRACTION98
2.2677-2.38720.27991380.21521602X-RAY DIFFRACTION99
2.3872-2.53660.291380.21471644X-RAY DIFFRACTION100
2.5366-2.73220.24391380.20681614X-RAY DIFFRACTION100
2.7322-3.00670.28521430.21551666X-RAY DIFFRACTION100
3.0067-3.44080.2311420.20781654X-RAY DIFFRACTION100
3.4408-4.33120.20321470.1641695X-RAY DIFFRACTION100
4.3312-24.67610.19651580.15761820X-RAY DIFFRACTION99
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)
11.4941-0.0344-0.90890.32850.95445.98660.1988-0.006-0.1550.11190.3919-0.22620.03241.4451-0.42510.4115-0.02070.02760.6364-0.09240.453138.82113.7197102.6374
25.51261.1669-2.10812.5547-1.8821.76680.1964-0.64390.08890.44560.2158-0.3428-1.08531.3002-0.36630.6199-0.27610.08660.6037-0.10770.460432.706121.6834117.5189
31.63712.2456-2.9273.2735-4.1265.26430.0512-0.26271.6341-0.11160.08650.1906-0.78061.1807-0.09341.3134-0.3660.08140.6614-0.03791.207732.052333.4542111.5662
4-0.5157-0.0907-1.45140.5543-0.21624.06850.22330.0782-0.07450.0202-0.11130.1616-0.5752-0.0143-0.16370.3055-0.03260.00860.4891-0.07810.383633.769515.548694.7836
54.48410.35810.72624.96731.24376.6563-0.03721.05380.7961-0.7009-0.08390.052-1.0021-0.51560.0550.41190.034-0.03160.69630.06230.430427.192618.24761.4412
64.4664-1.203-0.56511.5647-0.39693.15060.0350.15390.0317-0.0944-0.0173-0.0494-0.0087-0.01250.0050.2277-0.0069-0.00190.4663-0.05750.364932.069510.286669.1205
70.3997-0.0887-0.3290.2262-0.53651.20480.04880.0212-0.01330.018-0.03960.03260.05070.1088-00.3058-0.0284-0.00270.4276-0.05440.459832.721211.658285.3096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 377 THROUGH 421 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 422 THROUGH 443 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 444 THROUGH 453 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 454 THROUGH 491 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 492 THROUGH 508 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 509 THROUGH 581 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 601 THROUGH 734 )

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