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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 / homologySUI1 domain / PUA domain / PUA domain profile. / Translation initiation factor SUI1 family profile. / Translation initiation factor SUI1 / PUA domain superfamily / SWIB/MDM2 domain superfamily / SUI1 domain superfamily / PUA-like superfamily / IRES-dependent viral translational initiation ...SUI1 domain / PUA domain / PUA domain profile. / Translation initiation factor SUI1 family profile. / Translation initiation factor SUI1 / PUA domain superfamily / SWIB/MDM2 domain superfamily / SUI1 domain superfamily / PUA-like superfamily / IRES-dependent viral translational initiation / formation of translation preinitiation complex / ribosome disassembly / translation initiation factor activity / intracellular protein transport / signaling receptor activity / nuclear body / cytosol / cytoplasm / Eukaryotic translation initiation factor 2D
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 1.8 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 21, 2017 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Aug 9, 2017Structure modelDatabase referencescitation / citation_author_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
1.2Aug 16, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 2D


Theoretical massNumber of molelcules
Total (without water)23,2771
Polyers23,2771
Non-polymers00
Water2,414134
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)11680
MethodPISA
Unit cell
γ
α
β
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-MP 41 21 2

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Components

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


Mass: 23277.051 Da / Num. of mol.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 134 / Formula: H2O / Water

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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 / Density percent sol: 54.89 %
Crystal growTemp: 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, 25 mM sodium potassium tartrate, 10.7% PEG3350, 10.7% MPD, 10.7% PEG1000)

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Data collection

DiffractionMean temperature: 273 kelvins
SourceSource: SYNCHROTRON / Type: SLS BEAMLINE X06SA / Synchrotron site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Collection date: Sep 3, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 49.35 Å / Number obs: 24936 / CC half: 0.999 / Rmerge I obs: 0.057 / NetI over sigmaI: 14.9 / Redundancy: 6.9 % / Percent possible obs: 99.85
Reflection shellRmerge I obs: 1.026 / Highest resolution: 1.8 Å / Lowest resolution: 1.91 Å / CC half: 0.71 / Percent possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefineMethod to determine structure: SAD / Overall SU ML: 0.19 / Cross valid method: FREE R-VALUE / Sigma F: 0 / Overall phase error: 25.04 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.231 / R factor R work: 0.19 / R factor obs: 0.193 / Highest resolution: 1.8 Å / Lowest resolution: 24.67 Å / Number reflection R free: 1908 / Number reflection obs: 24173 / Percent reflection R free: 7.89 / Percent reflection obs: 96.9
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 24.67 Å
Number of atoms included #LASTProtein: 1604 / Nucleic acid: 0 / Ligand: 0 / Solvent: 134 / Total: 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
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.80010.30890.30041.8451117140888.00
1.84510.33630.27151.8950129143990.00
1.89500.26240.23841.9507127149192.00
1.95070.31680.23422.0136126152596.00
2.01360.28340.21662.0856134155997.00
2.08560.23940.20952.1690134157397.00
2.16900.26260.21902.2677137157598.00
2.26770.27990.21522.3872138160299.00
2.38720.29000.21472.53661381644100.00
2.53660.24390.20682.73221381614100.00
2.73220.28520.21553.00671431666100.00
3.00670.23100.20783.44081421654100.00
3.44080.20320.16404.33121471695100.00
4.33120.19650.157624.6761158182099.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.4941-0.0344-0.90890.32850.95445.98660.1988-0.0060-0.15500.11190.3919-0.22620.03241.4451-0.42510.4115-0.02070.02760.6364-0.09240.453138.821013.7197102.6374
25.51261.1669-2.10812.5547-1.88201.76680.1964-0.64390.08890.44560.2158-0.3428-1.08531.3002-0.36630.6199-0.27610.08660.6037-0.10770.460432.706121.6834117.5189
31.63712.2456-2.92703.2735-4.12605.26430.0512-0.26271.6341-0.11160.08650.1906-0.78061.1807-0.09341.3134-0.36600.08140.6614-0.03791.207732.052333.4542111.5662
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
54.48410.35810.72624.96731.24376.6563-0.03721.05380.7961-0.7009-0.08390.0520-1.0021-0.51560.05500.41190.0340-0.03160.69630.06230.430427.192618.247061.4412
64.4664-1.2030-0.56511.5647-0.39693.15060.03500.15390.0317-0.0944-0.0173-0.0494-0.0087-0.01250.00500.2277-0.0069-0.00190.4663-0.05750.364932.069510.286669.1205
70.3997-0.0887-0.32900.2262-0.53651.20480.04880.0212-0.01330.0180-0.03960.03260.05070.1088-0.00000.3058-0.0284-0.00270.4276-0.05440.459832.721211.658285.3096
Refine 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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