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- PDB-2wmc: Crystal structure of eukaryotic initiation factor 4E from Pisum s... -

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Basic information

Entry
Database: PDB / ID: 2wmc
TitleCrystal structure of eukaryotic initiation factor 4E from Pisum sativum
ComponentsEUKARYOTIC TRANSLATION INITIATION FACTOR 4EEIF4E
KeywordsBIOSYNTHETIC PROTEIN / INITIATION FACTOR / PROTEIN BIOSYNTHESIS / EIF4E / SBM1 GENE / RNA-BINDING / PISUM SATIVUM
Function / homology
Function and homology information


translation initiation factor activity / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / mRNA cap-binding protein
Similarity search - Component
Biological speciesPISUM SATIVUM (garden pea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAshby, J.A. / Stevenson, C.E.M. / Maule, A.J. / Lawson, D.M.
Citation
Journal: Plos One / Year: 2011
Title: Structure-Based Mutational Analysis of Eif4E in Relation to Sbm1 Resistance to Pea Seed-Borne Mosaic Virus in Pea.
Authors: Ashby, J.A. / Stevenson, C.E. / Jarvis, G.E. / Lawson, D.M. / Maule, A.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and Preliminary X-Ray Analysis of Eukaryotic Initiation Factor 4E from Pisum Sativum.
Authors: Ashby, J.A. / Stevenson, C.E.M. / Maule, A.J. / Lawson, D.M.
History
DepositionJun 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
G: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
H: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,10616
Polymers163,8018
Non-polymers4,3068
Water14,232790
1
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0132
Polymers20,4751
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0132
Polymers20,4751
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0132
Polymers20,4751
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0132
Polymers20,4751
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0132
Polymers20,4751
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0132
Polymers20,4751
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0132
Polymers20,4751
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0132
Polymers20,4751
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.612, 136.320, 74.415
Angle α, β, γ (deg.)90.00, 92.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.04555, 0.97435, -0.22037), (-0.72353, 0.18428, 0.66524), (0.68879, 0.12915, 0.71336)-62.07152, 29.50035, 11.83081
2given(-0.99872, -0.04807, -0.01549), (0.02374, -0.71751, 0.69615), (-0.04458, 0.69489, 0.71773)-37.93857, 83.45405, -33.44569
3given(-0.00488, -0.91866, 0.39502), (0.75795, 0.25428, 0.60071), (-0.65229, 0.30234, 0.69506)26.66482, 54.78761, -24.91273
4given(-0.18538, 0.88522, -0.42664), (-0.85148, 0.07202, 0.51942), (0.49053, 0.45957, 0.74039)-57.79124, 42.86471, -59.97589
5given(-0.98356, -0.10161, 0.1493), (0.17989, -0.47858, 0.85942), (-0.01587, 0.87214, 0.48899)2.00816, 50.45886, -66.6778
6given(0.11661, -0.93189, 0.34349), (0.94783, 0.20773, 0.2418), (-0.29669, 0.29737, 0.90749)24.31589, 9.76413, -42.26576
7given(0.99228, 0.12024, -0.03033), (-0.10514, 0.94545, 0.30832), (0.06574, -0.30275, 0.9508)-40.88003, -13.13385, -8.61153

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Components

#1: Protein
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF4E


Mass: 20475.092 Da / Num. of mol.: 8 / Fragment: N-TERMINALLY TRUNCATED FORM, RESIDUES 52-228
Source method: isolated from a genetically manipulated source
Details: CONTAINS RESIDUES 52-228 OF THE NATIVE SEQUENCE PLUS AN ADDITIONAL N-TERMINAL METHIONINE
Source: (gene. exp.) PISUM SATIVUM (garden pea) / Plasmid: PET24APLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA-2(DE3) / Variant (production host): PLYSS / References: UniProt: Q6TEC4
#2: Chemical
ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details7-METHYL-GUANOSINE-5P-TRIPHOSPHATE (MGP). TERMINAL PHOSPHATES MISSING IN THE COORDINATES - EITHER ...7-METHYL-GUANOSINE-5P-TRIPHOSPHATE (MGP). TERMINAL PHOSPHATES MISSING IN THE COORDINATES - EITHER HYDROLYZED OR DISORDERED
Sequence detailsCONTAINS RESIDUES 52-228 OF THE NATIVE SEQUENCE PLUS AN ADDITIONAL N-TERMINAL METHIONINE

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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: 2.28 Å3/Da / Density % sol: 46.09 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7 / Details: 18% (W/V) PEG 3350 IN 100 MM HEPES PH 7.0 AT 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 30, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→21.93 Å / Num. obs: 72233 / % possible obs: 97.4 % / Observed criterion σ(I): -9 / Redundancy: 3.73 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.64
Reflection shellResolution: 2.2→2.22 Å / Redundancy: 3.47 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.39 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IDV

2idv


Resolution: 2.2→136.083 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.31 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 3642 5.02 %RANDOM
Rwork0.1799 ---
obs0.183 72232 97.205 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.204 Å20 Å20.549 Å2
2---1.357 Å20 Å2
3---1.612 Å2
Refinement stepCycle: LAST / Resolution: 2.2→136.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10788 0 232 790 11810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211392
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.92415523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84451313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34224.477545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.918151704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3521523
X-RAY DIFFRACTIONr_chiral_restr0.0770.21568
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212564
X-RAY DIFFRACTIONr_gen_planes_other
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_other0.2410.255
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_it0.4351.56629
X-RAY DIFFRACTIONr_mcbond_other0.091.52730
X-RAY DIFFRACTIONr_mcangle_it0.801210601
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.25834763
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9834.54922
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 278 -
Rwork0.206 4954 -
obs--94.869 %
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)
11.06740.30760.09892.0282-0.45181.4449-0.05010.06890.0577-0.09750.0204-0.1585-0.08460.0220.0297-0.1225-0.0020.0271-0.12640.0089-0.146-3.521167.9589-2.9993
22.7059-1.4859-0.9772.98570.39971.57080.08880.05680.1471-0.097-0.1196-0.1664-0.02320.03540.0309-0.12420.01140.0003-0.10580.0444-0.1635-36.551261.78681.4492
31.8682-0.1162-0.43952.381-0.26021.7519-0.0422-0.0091-0.02910.08790.04860.13550.0639-0.1455-0.0064-0.122-0.0081-0.0226-0.1134-0.0189-0.1405-35.758430.617710.4544
42.391-0.41970.61382.7042-0.43751.3185-0.0073-0.1019-0.04610.04890.0131-0.1983-0.02240.0767-0.0059-0.1349-0.00670.0109-0.16240.002-0.1309-3.577237.908710.4285
53.0276-0.9333-0.44241.8031-0.02141.94590.0399-0.17160.13380.0936-0.03290.0955-0.11520.0002-0.0069-0.1105-0.01280.0013-0.1133-0.0095-0.0837-3.615675.229531.7599
63.60890.3955-0.47592.6138-0.94123.2536-0.057-0.07690.0230.17990.0220.2610.0266-0.21640.0351-0.04820.00210.041-0.0594-0.0023-0.04578.483547.152244.9151
73.5653-0.55220.45143.051-0.14651.6019-0.0118-0.3155-0.02070.40670.0525-0.08650.01820.1314-0.0407-0.03480.0279-0.0226-0.0876-0.0037-0.171340.157450.143139.5722
81.6544-0.26530.56632.46020.43471.565-0.1161-0.12930.17720.08920.0177-0.1047-0.16430.09150.0984-0.11130.00410.0019-0.1002-0.0075-0.081228.536678.954629.0678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 228
2X-RAY DIFFRACTION2B52 - 228
3X-RAY DIFFRACTION3C52 - 228
4X-RAY DIFFRACTION4D52 - 228
5X-RAY DIFFRACTION5E52 - 228
6X-RAY DIFFRACTION6F52 - 228
7X-RAY DIFFRACTION7G52 - 228
8X-RAY DIFFRACTION8H52 - 228

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