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- PDB-2jgb: Structure of human eIF4E homologous protein 4EHP with m7GTP -

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Basic information

Entry
Database: PDB / ID: 2jgb
TitleStructure of human eIF4E homologous protein 4EHP with m7GTP
Components
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TYPE 2
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1
KeywordsTRANSLATION / PHOSPHORYLATION / INITIATION FACTOR / 4EHP / EIF4E / RNA-BINDING / ACETYLATION / CAP-BINDING / EUKARYOTIC INITIATION FACTOR / 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 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / TOR signaling ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / TOR signaling / mTORC1-mediated signalling / translation repressor activity / translation initiation factor binding / negative regulation of translational initiation / rescue of stalled ribosome / translation initiation factor activity / positive regulation of mitotic cell cycle / translational initiation / P-body / ISG15 antiviral mechanism / G1/S transition of mitotic cell cycle / negative regulation of translation / ubiquitin protein ligase binding / RNA binding / 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
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 4E type 2 / Eukaryotic translation initiation factor 4E-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCameron, A.D. / Rosettani, P. / Knapp, S. / Vismara, M.G. / Rusconi, L.
CitationJournal: J. Mol. Biol. / Year: 2007
Title: Structures of the human eIF4E homologous protein, h4EHP, in its m7GTP-bound and unliganded forms.
Authors: Rosettani, P. / Knapp, S. / Vismara, M.G. / Rusconi, L. / Cameron, A.D.
History
DepositionFeb 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 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 TYPE 2
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1843
Polymers24,6442
Non-polymers5391
Water3,477193
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-11.2 kcal/mol
Surface area13560 Å2
MethodPQS
Unit cell
Length a, b, c (Å)43.499, 49.299, 103.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TYPE 2 / EIF4E TYPE 2 / EIF-4E TYPE 2 / MRNA CAP-BINDING PROTEIN TYPE 3 / EUKARYOTIC TRANSLATION INITIATION ...EIF4E TYPE 2 / EIF-4E TYPE 2 / MRNA CAP-BINDING PROTEIN TYPE 3 / EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-LIKE 3 / EUKARYOTIC TRANSLATION INITIATION FACTOR 4E HOMOLOGOUS PROTEIN / MRNA CAP-BINDING PROTEIN 4EHP / EIF4E-LIKE PROTEIN 4E-LP / EUKARYOTIC INITITIATION FACTOR 4E HOMOLOGOUS PROTEIN


Mass: 22499.787 Da / Num. of mol.: 1 / Fragment: RESIDUES 45-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60573
#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 ...4E-BP1 / EIF4E-BINDING PROTEIN 1 / PHOSPHORYLATED HEAT- AND ACID-STABLE PROTEIN REGULATED BY INSULIN 1 / PHAS-I / EIF4E BINDING PROTEIN


Mass: 2144.564 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-66 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q13541
#3: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE INITIAL GPLHM HAS BEEN INTRODUCED DURING THE CLONING. RESIDUES 44 TO 234 RESIDUES 51 TO 67

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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: 2.5 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 5.5
Details: 20% PEG-3000, 0.1M SODIUM CITRATE PH 5.5 WITH 1MM M7GTP IN THE DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 26, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 111967 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IPB

1ipb


Resolution: 1.7→51.92 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.315 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 225 TO 227 OF THE PROTEIN CANNOT BE OBSERVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1262 5 %RANDOM
Rwork0.202 ---
obs0.204 23859 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.49 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→51.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1665 0 33 193 1891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9662363
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42522.61984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5041517
X-RAY DIFFRACTIONr_chiral_restr0.0980.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021322
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2786
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21164
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2185
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1531.51047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69721640
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4923826
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9794.5723
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 102
Rwork0.309 1692

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