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- PDB-34ak: Homo sapiens Eukaryotic translation initiation factor 4E (eIF4E) ... -

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Basic information

Entry
Database: PDB / ID: 34ak
TitleHomo sapiens Eukaryotic translation initiation factor 4E (eIF4E) in complex with synthetic mRNA cap analogs
ComponentsEukaryotic translation initiation factor 4E
KeywordsRNA BINDING PROTEIN / complex with cap analogue
Function / homology
Function and homology information


translation repressor complex / eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / Transport of the SLBP independent Mature mRNA ...translation repressor complex / eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / mRNA cap binding / RNA 7-methylguanosine cap binding / Transport of Mature mRNA Derived from an Intronless Transcript / M-decay: degradation of maternal mRNAs by maternally stored factors / RISC complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / mRNA export from nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of mitotic cell cycle / translation initiation factor activity / excitatory synapse / G1/S transition of mitotic cell cycle / P-body / translational initiation / Dengue Virus Genome Translation and Replication / regulation of translation / ISG15 antiviral mechanism / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / DNA-binding transcription factor binding / postsynapse / nuclear speck / negative regulation of translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
ACETATE ION / Chem-V9G / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSchneider, S. / Schwarz, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other private Germany
CitationJournal: To Be Published
Title: Structural basis of eIF4E recognition of synthetic mRNA cap analogues links cap architecture to affinity and biological activity
Authors: Schneider, S. / Moreno, S. / Thran, M. / Schwarz, A.
History
DepositionSep 3, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release

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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)92,87710
Polymers89,5504
Non-polymers3,3276
Water5,152286
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2513
Polymers22,3871
Non-polymers8642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2483
Polymers22,3871
Non-polymers8612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1892
Polymers22,3871
Non-polymers8011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1892
Polymers22,3871
Non-polymers8011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.130, 38.148, 147.442
Angle α, β, γ (deg.)84.81, 88.81, 76.76
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Eukaryotic translation initiation factor 4E / eIF-4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein


Mass: 22387.451 Da / Num. of mol.: 4 / Mutation: del 1-27
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pET28 / Production host: Escherichia coli B (bacteria) / Strain (production host): T7 express / References: UniProt: P06730
#2: Chemical
ChemComp-V9G / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-ADENOSINE


Mass: 801.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H32N10O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 47.02 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% w/v PEG 4000 100mM HEPES; pH 7.5 100 mM Sodium acetate

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Data collection

DiffractionMean temperature: 281 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.05→48.95 Å / Num. obs: 50430 / % possible obs: 99.7 % / Redundancy: 14 % / CC1/2: 0.988 / Rmerge(I) obs: 0.364 / Rpim(I) all: 0.1 / Rrim(I) all: 0.378 / Χ2: 0.91 / Net I/σ(I): 5.7 / Num. measured all: 705898
Reflection shellResolution: 2.05→2.11 Å / % possible obs: 99.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 1.936 / Num. measured all: 44976 / Num. unique obs: 3989 / CC1/2: 0.74 / Rpim(I) all: 0.603 / Rrim(I) all: 2.031 / Χ2: 0.96 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→37.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.276 2505 5 %
Rwork0.226 --
obs-50362 99.6 %
Refinement stepCycle: LAST / Resolution: 2.05→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6077 0 216 286 6579

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