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- PDB-3tf2: Crystal structure of the cap free human translation initiation fa... -

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Basic information

Entry
Database: PDB / ID: 3tf2
TitleCrystal structure of the cap free human translation initiation factor eIF4E
ComponentsEukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION / eIF4E / mRNA export / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / : / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / : / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / Transport of the SLBP independent Mature mRNA / RNA 7-methylguanosine cap binding / Transport of the SLBP Dependant Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / stem cell population maintenance / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear speck / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / nucleus / cytosol / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSiddiqui, N. / Tempel, W. / Nedyalkova, L. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Borden, K.L.B. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural insights into the allosteric effects of 4EBP1 on the eukaryotic translation initiation factor eIF4E.
Authors: Siddiqui, N. / Tempel, W. / Nedyalkova, L. / Volpon, L. / Wernimont, A.K. / Osborne, M.J. / Park, H.W. / Borden, K.L.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)100,52118
Polymers100,5214
Non-polymers014
Water3,045169
1
A: Eukaryotic translation initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)25,1307
Polymers25,1301
Non-polymers06
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)25,1305
Polymers25,1301
Non-polymers04
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Eukaryotic translation initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)25,1304
Polymers25,1301
Non-polymers03
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Eukaryotic translation initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)25,1302
Polymers25,1301
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.236, 56.739, 100.310
Angle α, β, γ (deg.)103.610, 91.360, 110.140
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Eukaryotic translation initiation factor 4E / EIF4E / eIF-4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein


Mass: 25130.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P06730
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.4 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 20% PEG-3350, 0.2 M diammonium citrate, vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 44808 / % possible obs: 97.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.05 / Χ2: 1.1 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1420.37421900.909197
2.14-2.1820.30422770.79197.2
2.18-2.2220.29221690.85197.3
2.22-2.261.80.24621943.059195.1
2.26-2.311.90.28622141.016196.4
2.31-2.3720.18422280.874197.5
2.37-2.4220.18922210.877197.6
2.42-2.4920.14522650.934197.9
2.49-2.5620.13222490.949198
2.56-2.6520.10922500.957197.7
2.65-2.7420.09522370.991198
2.74-2.851.90.07622621.079198.2
2.85-2.981.90.06122371.039198.3
2.98-3.141.90.05122550.983198.4
3.14-3.331.90.0422751.077198.3
3.33-3.591.90.03322691.174198.6
3.59-3.951.90.03222351.518198.3
3.95-4.521.90.02722351.364198.5
4.52-5.71.90.02223060.919198.9
5.7-401.90.02222400.899198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modified coordinates of pdb entry 1IPB

1ipb


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.26 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED. Significant difference density is observed around gaps in protein chains C (residues 119-122) and D (residues 118- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED. Significant difference density is observed around gaps in protein chains C (residues 119-122) and D (residues 118-125) but is not interpretable in terms of peptide geometry. The program COOT and the MOLPROBITY server were also used in the course of model refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 1342 3.004 %THINSHELLS (SFTOOLS)
Rwork0.2154 ---
obs0.217 44671 97.716 %-
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 max: 83.87 Å2 / Biso mean: 29.854 Å2 / Biso min: 13.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.601 Å2-0.339 Å20.47 Å2
2---2.209 Å20.84 Å2
3---1.792 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 14 169 5764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215808
X-RAY DIFFRACTIONr_bond_other_d0.0010.023877
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9257910
X-RAY DIFFRACTIONr_angle_other_deg0.86239373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30323.763287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04415935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2831539
X-RAY DIFFRACTIONr_chiral_restr0.0810.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021270
X-RAY DIFFRACTIONr_mcbond_it0.6091.53499
X-RAY DIFFRACTIONr_mcbond_other0.1531.51425
X-RAY DIFFRACTIONr_mcangle_it1.06525617
X-RAY DIFFRACTIONr_scbond_it1.72232309
X-RAY DIFFRACTIONr_scangle_it2.5934.52283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1540.343610.2573138329697.057
2.154-2.2130.295570.2583166331597.225
2.213-2.2770.5281390.4012884321893.94
2.277-2.3460.336240.2342979307797.595
2.346-2.4230.3261580.2482771300497.503
2.423-2.5070.3571110.2422724290197.725
2.507-2.6010.283470.2452739284298.03
2.601-2.7070.2711400.2342499269897.813
2.707-2.82600.222576262398.208
2.826-2.9630.2521060.2112314246198.334
2.963-3.1210.2631030.2262203234598.337
3.121-3.3080.248140.2082204225798.272
3.308-3.5340.222970.1971966209598.473
3.534-3.8120.221700.1941849195198.36
3.812-4.1690.173530.171698178298.26
4.169-4.650.205520.1541571164198.903
4.65-5.3480.229430.1711390145098.828
5.348-6.4990.29250.2161198123698.948
6.499-8.9830.232310.22691194999.262
8.983-300.244110.21554957497.561
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)
11.7748-0.49430.55432.0235-0.29225.6614-0.14270.03110.03210.07260.04710.1301-0.5432-0.32350.09560.09990.0689-0.03230.0618-0.01510.073426.1465-26.76910.4988
21.69690.5092-0.87041.9495-0.19065.5917-0.1830.0267-0.1368-0.02830.03380.07620.47-0.36910.14920.0752-0.05760.04150.0571-0.01830.097728.6393-41.0687-27.1996
31.70810.1293-1.0593.1382-0.17785.29990.08250.10610.1806-0.1620.0240.2536-0.37120.0008-0.10650.0803-0.0480.00550.05880.00590.11639.9701-15.6656-37.454
41.596-0.11111.00964.2405-0.19625.25020.1423-0.1373-0.23710.16170.04560.1820.42690.026-0.18780.08820.0462-0.020.07070.00830.098638.0048-52.372620.5936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 217
2X-RAY DIFFRACTION1A218 - 267
3X-RAY DIFFRACTION2B35 - 217
4X-RAY DIFFRACTION2B218 - 261
5X-RAY DIFFRACTION3C33 - 217
6X-RAY DIFFRACTION3C218 - 258
7X-RAY DIFFRACTION4D35 - 217
8X-RAY DIFFRACTION4D218 - 251

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