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- PDB-2v8y: Crystallographic and mass spectrometric characterisation of eIF4E... -

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Basic information

Entry
Database: PDB / ID: 2v8y
TitleCrystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives
Components
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4EEIF4E
KeywordsTRANSLATION / PHOSPHORYLATION / INITIATION FACTOR / CAP / EIF4E / 7BNGMP / 4E-BP1 / RNA-BINDING / ACETYLATION / HOST-VIRUS INTERACTION / PROTEIN SYNTHESIS INHIBITOR / PROTEIN BIOSYNTHESIS / TRANSLATION REGULATION
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 / eukaryotic initiation factor 4E 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 / : ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E 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 / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / 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 / TOR signaling / 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 / translation initiation factor binding / negative regulation of translational initiation / translation repressor activity / translational initiation / translation initiation factor activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / P-body / G1/S transition of mitotic cell cycle / cytoplasmic ribonucleoprotein granule / ISG15 antiviral mechanism / neuron differentiation / cytoplasmic stress 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
Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / 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
P-FLUORO-7-BENZYL GUANINE MONOPHOSPHATE / Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4E-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrown, C.J. / Mcnae, I. / Fischer, P.M. / Walkinshaw, M.D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystallographic and Mass Spectrometric Characterisation of Eif4E with N(7)-Alkylated CAP Derivatives.
Authors: Brown, C.J. / Mcnae, I. / Fischer, P.M. / Walkinshaw, M.D.
History
DepositionAug 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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-BINDING PROTEIN 1
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9286
Polymers53,9834
Non-polymers9452
Water5,621312
1
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4643
Polymers26,9912
Non-polymers4721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-8.4 kcal/mol
Surface area12100 Å2
MethodPQS
2
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4643
Polymers26,9912
Non-polymers4721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-8.5 kcal/mol
Surface area12460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)38.438, 100.731, 135.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.72414, 0.443, -0.52856), (0.51943, -0.8545, -0.00454), (-0.45367, -0.27126, -0.84888)0.03837, 34.94394, 79.56729
2given(0.72414, 0.51943, -0.45367), (0.443, -0.8545, -0.27126), (-0.52856, -0.00454, -0.84888)17.91839, 51.42598, 67.72248

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF4E / EIF4E / EIF-4E / MRNA CAP-BINDING PROTEIN / EIF-4F 25 KDA SUBUNIT


Mass: 25130.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET11D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PLYSS ROSETTA / References: UniProt: P06730
#2: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1 / 4E-BP1 / EIF4E-BINDING PROTEIN 1 / PHOSPHORYLATED HEAT- AND ACID-STABLE PROTEIN REGULATED BY INSULIN 1 /


Mass: 1861.240 Da / Num. of mol.: 2 / Fragment: PHAS-I4E-BP1 BINDING PEPTIDE, RESIDUES 50-63 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q13541
#3: Chemical ChemComp-MGV / P-FLUORO-7-BENZYL GUANINE MONOPHOSPHATE


Type: RNA linking / Mass: 472.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20FN5O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.62 Å3/Da / Density % sol: 53.08 % / Description: NONE
Crystal growpH: 7
Details: 25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.48
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 2.1→41.17 Å / Num. obs: 28510 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.3 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EJH

1ejh


Resolution: 2.1→25.3 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.956 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1468 5.2 %RANDOM
Rwork0.203 ---
obs0.206 27012 90.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 64 312 3622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223393
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9594591
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17223.276174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72415599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.811530
X-RAY DIFFRACTIONr_chiral_restr0.1330.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022576
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21528
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22250
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3220.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9931.51984
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.723110
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.35731695
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6634.51481
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 100
Rwork0.24 1870

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