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- PDB-5me7: Crystal Structure of eiF4E from C. melo -

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Basic information

Entry
Database: PDB / ID: 5me7
TitleCrystal Structure of eiF4E from C. melo
ComponentsEukaryotic transcription initiation factor 4E
KeywordsTRANSLATION / eIF4E / C. melo
Function / homology
Function and homology information


eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translational initiation / translation initiation factor activity / 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
Eukaryotic translation initiation factor 4E-1
Similarity search - Component
Biological speciesCucumis melo (muskmelon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 1.1May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)85,8569
Polymers85,3964
Non-polymers4605
Water2,558142
1
A: Eukaryotic transcription initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4412
Polymers21,3491
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic transcription initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4412
Polymers21,3491
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic transcription initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6254
Polymers21,3491
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic transcription initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)21,3491
Polymers21,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.746, 108.957, 122.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAMETMETAA53 - 2344 - 185
21ALAALAMETMETBB53 - 2344 - 185
12ASNASNVALVALAA51 - 2352 - 186
22ASNASNVALVALCC51 - 2352 - 186
13ALAALAVALVALAA52 - 2353 - 186
23ALAALAVALVALDD52 - 2353 - 186
14ALAALAVALVALBB53 - 2354 - 186
24ALAALAVALVALCC53 - 2354 - 186
15ALAALAVALVALBB53 - 2354 - 186
25ALAALAVALVALDD53 - 2354 - 186
16ALAALAVALVALCC52 - 2353 - 186
26ALAALAVALVALDD52 - 2353 - 186

NCS ensembles :
ID
1
2
3
4
5
6

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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 BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: Q00LS8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C3H8O3 / Source: (gene. exp.) Cucumis melo (muskmelon) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting 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: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→81.31 Å / Num. obs: 39619 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rsym value: 0.103 / Net I/av σ(I): 4 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.323.60.3842197.8
2.32-2.463.80.2822.6199.7
2.46-2.633.70.2123.4199.8
2.63-2.843.60.1534.6199.6
2.84-3.113.80.1165.4199.9
3.11-3.483.70.0955.8199.4
3.48-4.023.70.0896.2199.4
4.02-4.923.70.0866.5199.3
4.92-6.963.50.0856.6199.3
6.96-47.083.40.0875.8198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.21data scaling
XDSdata reduction
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.595 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21392 1985 5 %RANDOM
Rwork0.18671 ---
obs0.1881 37628 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.734 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å20 Å2
2--1.95 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 30 142 5880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195920
X-RAY DIFFRACTIONr_bond_other_d0.0120.025337
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9028024
X-RAY DIFFRACTIONr_angle_other_deg1.917312290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8025695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52524.348299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37715930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8611519
X-RAY DIFFRACTIONr_chiral_restr0.1310.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0216744
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021505
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7962.6972804
X-RAY DIFFRACTIONr_mcbond_other1.7922.6962803
X-RAY DIFFRACTIONr_mcangle_it2.8454.0313491
X-RAY DIFFRACTIONr_mcangle_other2.8464.0313492
X-RAY DIFFRACTIONr_scbond_it2.5823.0423116
X-RAY DIFFRACTIONr_scbond_other2.5823.0423116
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.084.424534
X-RAY DIFFRACTIONr_long_range_B_refined5.89721.9136584
X-RAY DIFFRACTIONr_long_range_B_other5.88621.8196548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A185640.11
12B185640.11
21A188140.09
22C188140.09
31A184380.1
32D184380.1
41B183700.1
42C183700.1
51B182640.11
52D182640.11
61C179520.1
62D179520.1
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 139 -
Rwork0.26 2619 -
obs--95.56 %
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)
12.342-0.7278-1.25122.070.81273.24260.03990.3044-0.0624-0.1586-0.16670.20820.132-0.35590.12680.0504-0.0012-0.03630.0964-0.05620.1091-14.78242.9772-16.7989
21.90070.1977-0.01573.4873-0.07211.62670.03810.159-0.0683-0.1111-0.0186-0.1550.02750.2064-0.01960.00610.0132-0.00460.13590.00890.1104-41.994123.5281-14.9446
32.63720.11080.03572.3616-0.1132.7617-0.005-0.02160.017-0.0383-0.02650.2771-0.1554-0.18830.03150.04110.0028-0.00970.0620.04090.1352-10.843841.0084-20.4629
42.0617-0.76650.30393.3286-0.26442.004-0.1262-0.33460.35890.4209-0.01170.039-0.4806-0.07320.13790.58360.0005-0.03650.2498-0.07230.2372-18.565116.0251-53.013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A51 - 235
2X-RAY DIFFRACTION2B53 - 235
3X-RAY DIFFRACTION3C51 - 235
4X-RAY DIFFRACTION4D51 - 235

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