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- PDB-5abu: Complex of D. melanogaster eIF4E with the 4E-binding protein Mext... -

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Basic information

Entry
Database: PDB / ID: 5abu
TitleComplex of D. melanogaster eIF4E with the 4E-binding protein Mextli and cap analog
Components
  • 4E-BINDING PROTEIN MEXTLI
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN
Function / homology
Function and homology information


TOR signaling pathway / Deadenylation of mRNA / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation / Ribosomal scanning and start codon recognition ...TOR signaling pathway / Deadenylation of mRNA / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation / Ribosomal scanning and start codon recognition / muscle cell postsynaptic specialization / RNA metabolic process / neuronal ribonucleoprotein granule / cap-dependent translation initiation factor activity / eukaryotic initiation factor 4G binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / cytoplasmic translational initiation / translation initiation factor activity / neuromuscular junction / translational initiation / P-body / nuclear body / translation / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / Eukaryotic translation initiation factor 4E1 / Uncharacterized protein
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPeter, D. / Weichenrieder, O.
CitationJournal: Genes Dev. / Year: 2015
Title: Mextli Proteins Use Both Canonical Bipartite and Novel Tripartite Binding Modes to Form Eif4E Complexes that Display Differential Sensitivity to 4E-BP Regulation
Authors: Peter, D. / Weber, R. / Koene, C. / Chung, M.-Y. / Ebertsch, L. / Truffault, V. / Weichenrieder, O. / Igreja, C. / Izaurralde, E.
History
DepositionAug 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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: 4E-BINDING PROTEIN MEXTLI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3134
Polymers29,4742
Non-polymers8392
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-26.8 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.880, 56.400, 99.080
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 / EIF-4E / EIF4E / EIF-4F 25 KDA SUBUNIT / MRNA CAP-BINDING PROT PROTEIN


Mass: 21249.037 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 69-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P48598
#2: Protein 4E-BINDING PROTEIN MEXTLI


Mass: 8225.225 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 577-640
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9VR35
#3: Chemical ChemComp-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O18P3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNUMBERING OF CHAIN A CORRESPONDS TO UNP P48598-2. COMPARED TO UNP P48598, SEQUENCE NUMBERS ARE ...NUMBERING OF CHAIN A CORRESPONDS TO UNP P48598-2. COMPARED TO UNP P48598, SEQUENCE NUMBERS ARE SHIFTED BY -11 RESIDUES. THE FIRST FOUR RESIDUES OF CHAIN A REMAIN FROM THE EXPRESSION TAG. THE FIRST SIX RESIDUES OF CHAIN B REMAIN FROM THE EXPRESSION TAG.

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 4
Details: 0.1M MMT (MALIC ACID:MES:TRIS), PH=4.0, 23% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.16→48.6 Å / Num. obs: 14107 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 35.84 Å2 / Rsym value: 0.12 / Net I/σ(I): 9
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.56 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UE8 CHAIN A

4ue8


Resolution: 2.16→40.882 Å / SU ML: 0.23 / σ(F): 1.38 / Phase error: 24.4 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 67, 68, 150, 190, 237, 243. THE FOLLOWING RESIDUES WERE ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 67, 68, 150, 190, 237, 243. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUES 73, 215. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 151 TO 153, 238 TO 241. CHAIN B, RESIDUES 636 TO 640. RESTRAINTS FOR THE GTG LIGAND WERE GENERATED WITH GRADE.
RfactorNum. reflection% reflection
Rfree0.2375 739 5.3 %
Rwork0.1946 --
obs0.197 13971 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.7 Å2
Refinement stepCycle: LAST / Resolution: 2.16→40.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 53 81 2033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022015
X-RAY DIFFRACTIONf_angle_d0.6032745
X-RAY DIFFRACTIONf_dihedral_angle_d10.574761
X-RAY DIFFRACTIONf_chiral_restr0.025293
X-RAY DIFFRACTIONf_plane_restr0.002370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.32680.29891440.23082581X-RAY DIFFRACTION99
2.3268-2.56090.26861320.22342624X-RAY DIFFRACTION100
2.5609-2.93140.27941520.20432614X-RAY DIFFRACTION100
2.9314-3.69290.24061470.19652658X-RAY DIFFRACTION100
3.6929-40.88880.20771640.17752755X-RAY DIFFRACTION99

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