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- PDB-1ejh: EIF4E/EIF4G PEPTIDE/7-METHYL-GDP -

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Basic information

Entry
Database: PDB / ID: 1ejh
TitleEIF4E/EIF4G PEPTIDE/7-METHYL-GDP
Components
  • EUKARYOTIC INITIATION FACTOR 4E
  • EUKARYOTIC INITIATION FACTOR 4GII
KeywordsTRANSLATION / eIF4E/eIF4GII peptide/7-methyl-GDP
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission / eukaryotic translation initiation factor 4F complex / chromatoid body / mRNA cap binding / RNA 7-methylguanosine cap binding / RISC complex / nuclear export / stem cell population maintenance / negative regulation of neuron differentiation / TOR signaling / mTORC1-mediated signalling / cellular response to dexamethasone stimulus / behavioral fear response / mRNA export from nucleus / translation initiation factor binding / translation repressor activity / translation initiation factor activity / negative regulation of translational initiation / positive regulation of mitotic cell cycle / translational initiation / P-body / G1/S transition of mitotic cell cycle / neuron differentiation / cytoplasmic stress granule / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear speck / nuclear body / translation / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / nucleus / cytoplasm / cytosol
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
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / : / Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4E-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsMarcotrigiano, J. / Gingras, A.-C. / Sonenberg, N. / Burley, S.K.
CitationJournal: Mol.Cell / Year: 1999
Title: Cap-dependent translation initiation in eukaryotes is regulated by a molecular mimic of eIF4G.
Authors: Marcotrigiano, J. / Gingras, A.C. / Sonenberg, N. / Burley, S.K.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Mar 6, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,61512
Polymers96,7828
Non-polymers1,8334
Water2,000111
1
A: EUKARYOTIC INITIATION FACTOR 4E
E: EUKARYOTIC INITIATION FACTOR 4GII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6543
Polymers24,1952
Non-polymers4581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-10 kcal/mol
Surface area10090 Å2
MethodPISA
2
B: EUKARYOTIC INITIATION FACTOR 4E
F: EUKARYOTIC INITIATION FACTOR 4GII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6543
Polymers24,1952
Non-polymers4581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-12 kcal/mol
Surface area9940 Å2
MethodPISA
3
C: EUKARYOTIC INITIATION FACTOR 4E
G: EUKARYOTIC INITIATION FACTOR 4GII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6543
Polymers24,1952
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-10 kcal/mol
Surface area9940 Å2
MethodPISA
4
D: EUKARYOTIC INITIATION FACTOR 4E
H: EUKARYOTIC INITIATION FACTOR 4GII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6543
Polymers24,1952
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-9 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.600, 140.60, 39.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
EUKARYOTIC INITIATION FACTOR 4E


Mass: 22145.113 Da / Num. of mol.: 4 / Fragment: 28-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET3B / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Protein/peptide
EUKARYOTIC INITIATION FACTOR 4GII


Mass: 2050.335 Da / Num. of mol.: 4 / Fragment: 622-637 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS)
References: GenBank: 2895097, UniProt: Q13541*PLUS
#3: Chemical
ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: (NH4)2SO4 and Peg400, pH 8.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0-2.1 Mammonium sulfate1reservoir
25 %PEG4001reservoir
310 mMEDTA1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Oct 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 44216 / % possible obs: 98.9 % / Observed criterion σ(I): 5 / Redundancy: 3 % / Rmerge(I) obs: 0.093
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.206 / % possible all: 95.8
Reflection shell
*PLUS
% possible obs: 95.8 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→20 Å / σ(F): 2 /
RfactorSelection details
Rfree0.261 10% data
Rwork0.218 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6254 0 116 111 6481
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.29
X-RAY DIFFRACTIONx_bond_d0.007
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.29

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