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- PDB-6ylt: Translation initiation factor 4E in complex with 3-MeBn7GpppG mRN... -

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Basic information

Entry
Database: PDB / ID: 6ylt
TitleTranslation initiation factor 4E in complex with 3-MeBn7GpppG mRNA 5' cap analog
ComponentsEukaryotic translation initiation factor 4E
KeywordsTRANSLATION / cap analog / translation initiation factor / 3-MeBn7GpppG / protein-ligand complex / eIF4E
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 / 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 / cellular response to dexamethasone stimulus / behavioral fear response / mRNA export from nucleus / translation initiation factor activity / 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
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
Chem-P3E / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsKubacka, D. / Wojcik, R. / Baranowski, M.R. / Kowalska, J. / Jemielity, J.
Funding support Poland, 2items
OrganizationGrant numberCountry
Foundation for Polish ScienceTEAM/2016_2/13 Poland
Polish National Science CentreUMO- 2017/24/C/NZ1/00169 Poland
CitationJournal: Pharmaceutics / Year: 2021
Title: Novel N7-Arylmethyl Substituted Dinucleotide mRNA 5' cap Analogs: Synthesis and Evaluation as Modulators of Translation.
Authors: Wojcik, R. / Baranowski, M.R. / Markiewicz, L. / Kubacka, D. / Bednarczyk, M. / Baran, N. / Wojtczak, A. / Sikorski, P.J. / Zuberek, J. / Kowalska, J. / Jemielity, J.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.country / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6798
Polymers89,1054
Non-polymers3,5744
Water4,035224
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1702
Polymers22,2761
Non-polymers8941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1702
Polymers22,2761
Non-polymers8941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1702
Polymers22,2761
Non-polymers8941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1702
Polymers22,2761
Non-polymers8941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.300, 38.330, 148.760
Angle α, β, γ (deg.)83.993, 87.776, 76.809
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUTHRTHR(chain 'A' and ((resid 32 through 33 and (name N...AA32 - 2036 - 177
12LYSLYSVALVAL(chain 'A' and ((resid 32 through 33 and (name N...AA212 - 217186 - 191
23GLUGLUTHRTHR(chain 'B' and (resid 32 through 48 or (resid 49...BB32 - 2036 - 177
24LYSLYSVALVAL(chain 'B' and (resid 32 through 48 or (resid 49...BB212 - 217186 - 191
35GLUGLUTHRTHR(chain 'C' and ((resid 32 through 33 and (name N...CC32 - 2036 - 177
36LYSLYSVALVAL(chain 'C' and ((resid 32 through 33 and (name N...CC212 - 217186 - 191
47GLUGLUTHRTHR(chain 'D' and (resid 32 through 55 or (resid 56...DD32 - 2036 - 177
48LYSLYSVALVAL(chain 'D' and (resid 32 through 55 or (resid 56...DD212 - 217186 - 191

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Components

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


Mass: 22276.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4e / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Chemical
ChemComp-P3E / [[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-7-[(3-methylphenyl)methyl]-6-oxidanylidene-1~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 893.563 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C28H36N10O18P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate tribasic pH 5.5, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.67→49.31 Å / Num. obs: 23009 / % possible obs: 98.92 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.8 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.1339 / Rpim(I) all: 0.07769 / Rrim(I) all: 0.1554 / Net I/σ(I): 9.76
Reflection shellResolution: 2.67→2.766 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2275 / CC1/2: 0.673 / CC star: 0.897 / Rpim(I) all: 0.3833 / Rrim(I) all: 0.7297 / % possible all: 96.77

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8B

1l8b


Resolution: 2.67→49.31 Å / SU ML: 0.3141 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.6767
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 849 3.69 %
Rwork0.2003 22147 -
obs0.2021 22996 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.52 Å2
Refinement stepCycle: LAST / Resolution: 2.67→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5681 0 198 224 6103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00776218
X-RAY DIFFRACTIONf_angle_d0.93428553
X-RAY DIFFRACTIONf_chiral_restr0.4188923
X-RAY DIFFRACTIONf_plane_restr0.00361045
X-RAY DIFFRACTIONf_dihedral_angle_d17.7721921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.840.34981390.25423607X-RAY DIFFRACTION97.63
2.84-3.060.24711410.2353706X-RAY DIFFRACTION99.61
3.06-3.360.26621430.19733722X-RAY DIFFRACTION99.38
3.36-3.850.26181430.18543743X-RAY DIFFRACTION98.86
3.85-4.850.2141420.17333710X-RAY DIFFRACTION99.61
4.85-49.310.21851410.20893659X-RAY DIFFRACTION98.45

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