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- PDB-5me6: Crystal Structure of eiF4E from C. melo bound to a CAP analog -

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Basic information

Entry
Database: PDB / ID: 5me6
TitleCrystal Structure of eiF4E from C. melo bound to a CAP analog
ComponentsEukaryotic transcription initiation factor 4E
KeywordsTRANSLATION / eIF4E / CAP analog / C. melo
Function / homology
Function and homology information


translation initiation factor activity / translational initiation / defense response to virus / RNA binding / nucleus / cytoplasm
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Eukaryotic translation initiation factor 4E-1
Similarity search - Component
Biological speciesCucumis melo (muskmelon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsQuerol-Audi, J. / Silva, C. / Miras, M. / Aranda-Regules, M. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
MINECOAGL2015-65838 Spain
CitationJournal: Plant Physiol. / Year: 2017
Title: Structure of eIF4E in Complex with an eIF4G Peptide Supports a Universal Bipartite Binding Mode for Protein Translation.
Authors: Miras, M. / Truniger, V. / Silva, C. / Verdaguer, N. / Aranda, M.A. / Querol-Audi, J.
History
DepositionNov 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic transcription initiation factor 4E
B: Eukaryotic transcription initiation factor 4E
C: Eukaryotic transcription initiation factor 4E
D: Eukaryotic transcription initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3126
Polymers85,3964
Non-polymers9162
Water00
1
A: Eukaryotic transcription initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8072
Polymers21,3491
Non-polymers4581
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic transcription initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)21,3491
Polymers21,3491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic transcription initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)21,3491
Polymers21,3491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic transcription initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8072
Polymers21,3491
Non-polymers4581
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.699, 108.868, 122.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Eukaryotic transcription initiation factor 4E / Eukaryotic translation initiation factor 4E


Mass: 21348.967 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucumis melo (muskmelon) / Production host: Escherichia coli (E. coli) / References: UniProt: Q00LS8
#2: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H18N5O11P2 / Source: (gene. exp.) Cucumis melo (muskmelon) / Production host: Escherichia coli (E. coli)

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.564→81.475 Å / Num. all: 24722 / Num. obs: 24722 / % possible obs: 96.7 % / Redundancy: 5.1 % / Rpim(I) all: 0.12 / Rrim(I) all: 0.274 / Rsym value: 0.244 / Net I/av σ(I): 2.241 / Net I/σ(I): 4.2 / Num. measured all: 125316
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.56-2.74.80.8810.81356128440.4280.9840.8811.578.2
2.7-2.874.90.68711731535120.3310.7660.6872.199.9
2.87-3.065.30.5491.21727032400.2580.6090.5492.7100
3.06-3.315.30.3991.61616430620.1930.4450.3993.799.9
3.31-3.634.90.2852.21398128250.1470.3220.2854.799.8
3.63-4.055.30.2272.71351525530.1130.2550.2275.999.9
4.05-4.685.30.1823.21206222900.0890.2040.1826.999.8
4.68-5.734.80.1653.6939919460.0830.1860.1656.699.7
5.73-8.115.10.1693.5794215460.0820.1890.1696.3100
8.11-47.0874.50.1423.641079040.0720.160.1427.499

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.867 / SU B: 43.013 / SU ML: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.453
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 869 4.9 %RANDOM
Rwork0.2201 ---
obs0.2222 16831 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.57 Å2 / Biso mean: 52.133 Å2 / Biso min: 20.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å20 Å2
2--2.16 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5653 0 58 0 5711
Biso mean--70.93 --
Num. residues----696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195900
X-RAY DIFFRACTIONr_bond_other_d0.0020.025282
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9118018
X-RAY DIFFRACTIONr_angle_other_deg1.061312164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7225688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21124.324296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94115922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8251519
X-RAY DIFFRACTIONr_chiral_restr0.1150.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216706
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021501
X-RAY DIFFRACTIONr_mcbond_it0.7041.7062776
X-RAY DIFFRACTIONr_mcbond_other0.7041.7062775
X-RAY DIFFRACTIONr_mcangle_it1.2332.5563456
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 65 -
Rwork0.297 1179 -
all-1244 -
obs--99.52 %
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)
12.668-0.5406-1.58142.12961.38113.70610.11010.307-0.0666-0.1716-0.1440.17650.0634-0.58670.03390.06170.0021-0.06750.1188-0.08580.4316-14.76562.8455-16.8726
22.51250.46620.50944.2891-0.38841.9438-0.01490.2866-0.1188-0.1214-0.0429-0.14270.05130.22510.05780.00880.01970.02080.1132-0.01460.3544-41.797823.3508-15.0363
32.03760.26390.07442.81240.45824.1499-0.0699-0.07140.00660.1130.07140.2552-0.1643-0.3982-0.00150.07080.0486-0.00180.11130.02360.4876-10.610240.845-20.4162
42.6412-1.19810.71343.5058-0.55454.491-0.2583-0.45350.380.91130.12470.0009-0.49-0.14430.13360.8490.00120.01710.2611-0.11640.654-20.092116.8163-53.6708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A51 - 1000
2X-RAY DIFFRACTION2B53 - 235
3X-RAY DIFFRACTION3C54 - 235
4X-RAY DIFFRACTION4D55 - 1000

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