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1ipb

CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GPPPA

Method: X-RAY DIFFRACTION Dmax: 47.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

EUKARYOTIC TRANSLATION INITIATION FACTOR 4E

Homo sapiens

UniProt P06730

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–217 Not recorded GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å R-free 0.229

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1IPB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IPC CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GTP Deposited 2001-05-08 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–217（217 aa）
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.228
1WKW Crystal structure of the ternary complex of eIF4E-m7GpppA-4EBP1 peptide Deposited 2004-06-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–217（191 aa） Fragment：RESIDUES 27-217
Not recorded GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 4000, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.270
2GPQ Cap-free structure of eIF4E suggests basis for its allosteric regulation Deposited 2006-04-18 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–217（217 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；293 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient
NMR sample composition 0.3mM eIF4E U-98% 15N, U-13C; 50mM phosphate buffer; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O | 50mM phosphate buffer; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O
NMR sample composition 0.3mM eIF4E U-98% 15N, U-95% D; 50mM phosphate buffer; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O | 50mM phosphate buffer; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O
Resolution not provided
2V8W Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7
Resolution 2.30 Å R-free 0.243
2V8W Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–217（217 aa）
Not recorded MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7
Resolution 2.30 Å R-free 0.243
2V8X Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded MGQ 7-BENZYL GUANINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0
Resolution 2.30 Å R-free 0.259
2V8X Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–217（217 aa）
Not recorded MGQ 7-BENZYL GUANINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0
Resolution 2.30 Å R-free 0.259
2V8Y Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded MGV P-FLUORO-7-BENZYL GUANINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0
Resolution 2.10 Å R-free 0.250
2V8Y Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–217（217 aa）
Not recorded MGV P-FLUORO-7-BENZYL GUANINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0
Resolution 2.10 Å R-free 0.250
2W97 Crystal Structure of eIF4E Bound to Glycerol and eIF4G1 peptide Deposited 2009-01-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–217（217 aa）
Chain B 1–217（217 aa）
Not recorded MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；60% AMMONIUM SULPHATE, 100MM TRIS-HCL PH 8.0, 1% PEG400
Resolution 2.29 Å R-free 0.239
3AM7 Crystal structure of the ternary complex of eIF4E-M7GTP-4EBP2 peptide Deposited 2010-08-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–217（191 aa） Fragment：UNP RESIDUES 27-217
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；20% PEG-MME 2000, 0.1M MES, 0.2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 2.20 Å R-free 0.268
3TF2 Crystal structure of the cap free human translation initiation factor eIF4E Deposited 2011-08-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–217（217 aa）
Not recorded UNX UNKNOWN LIGAND × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；20% PEG-3350, 0.2 M diammonium citrate, vapor diffusion, temperature 289K
Resolution 2.10 Å R-free 0.260
3TF2 Crystal structure of the cap free human translation initiation factor eIF4E Deposited 2011-08-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–217（217 aa）
Not recorded UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；20% PEG-3350, 0.2 M diammonium citrate, vapor diffusion, temperature 289K
Resolution 2.10 Å R-free 0.260
3TF2 Crystal structure of the cap free human translation initiation factor eIF4E Deposited 2011-08-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–217（217 aa）
Not recorded UNX UNKNOWN LIGAND × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；20% PEG-3350, 0.2 M diammonium citrate, vapor diffusion, temperature 289K
Resolution 2.10 Å R-free 0.260
3TF2 Crystal structure of the cap free human translation initiation factor eIF4E Deposited 2011-08-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–217（217 aa）
Not recorded UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；20% PEG-3350, 0.2 M diammonium citrate, vapor diffusion, temperature 289K
Resolution 2.10 Å R-free 0.260
3U7X Crystal structure of the human eIF4E-4EBP1 peptide complex without cap Deposited 2011-10-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium HEPES), vapor diffusion, sitting drop, temperature 291K
Resolution 2.10 Å R-free 0.224
3U7X Crystal structure of the human eIF4E-4EBP1 peptide complex without cap Deposited 2011-10-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–217（217 aa）
Not recorded SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium HEPES), vapor diffusion, sitting drop, temperature 291K
Resolution 2.10 Å R-free 0.224
3U7X Crystal structure of the human eIF4E-4EBP1 peptide complex without cap Deposited 2011-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–217（217 aa）
Chain B 1–217（217 aa）
Not recorded SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium HEPES), vapor diffusion, sitting drop, temperature 291K
Resolution 2.10 Å R-free 0.224
4AZA Improved eIF4E binding peptides by phage display guided design. Deposited 2012-06-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；20% PEG 5000 MME, 100 MM BISTRIS PH 6.5.
Resolution 2.16 Å R-free 0.279
4AZA Improved eIF4E binding peptides by phage display guided design. Deposited 2012-06-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–217（217 aa）
Not recorded MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；20% PEG 5000 MME, 100 MM BISTRIS PH 6.5.
Resolution 2.16 Å R-free 0.279
4BEA Crystal Structure of eIF4E in Complex with a Stapled Peptide Derivative Deposited 2013-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；18-26% OF POLYETHYLENE GLYCOL 3350, 0.01-02M AMMONIUM SULPHATE AND 100MM BIS-TRIS AT PH 5.5
Resolution 2.57 Å R-free 0.266
4DT6 Co-crystal structure of eIF4E with inhibitor Deposited 2012-02-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–217（217 aa）
Not recorded 6LI 7-[2-(4-chlorophenoxy)ethyl]guanosine 5'-(dihydrogen phosphate) × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；The purified protein which contained 100 uM m7-GTP was concentrated to about 7 mg/mL in 20 mM Hepes, pH 7.6, 100 mM KCl, 1mM DTT, and 0.1 mM EDTA for crystallization. The m7-GTP-bound eIF4e protein was crystallized with 1:1 ratio of protein solution to reservoir solution of 17-20% PEG-3350 and 0.1-0.4M Na formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.267
4DUM Co-crystal structure of eIF4E with inhibitor Deposited 2012-02-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–217（217 aa）
Not recorded HLI (4-{7-[2-(4-chlorophenoxy)ethyl]-2-(methylamino)-6-oxo-6,7-dihydro-1H-purin-8-yl}phenyl)phosphonic acid × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；The purified protein which contained 100 uM m7-GTP was then concentrated to about 7 mg/mL in 20 mM Hepes, pH7.6, 100 mM KCl, 1mM DTT, 0.1 mM EDTA for crystallization. The m7-GTP-bound eIF4e protein was crystallized with 1:1 ratio of protein solution to reservoir solution of 17-20% PEG-3350 and 0.1-0.4M Na formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.95 Å R-free 0.271
4TPW The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 33R (2E)-2-{2-[(4P)-4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]hydrazinylidene}-3-(2-nitrophenyl)propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；PEG 4000 10-20%, 100mM MES pH 6.5, 10% IPN
Resolution 1.50 Å R-free 0.193
4TPW The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；PEG 4000 10-20%, 100mM MES pH 6.5, 10% IPN
Resolution 1.50 Å R-free 0.193
4TQB The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 34K (2E)-2-{2-[4-(4-bromophenyl)-1,3-thiazol-2-yl]hydrazinylidene}-3-(2-nitrophenyl)propanoic acid × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；PEG 4000 12-20%, 100mM MES pH 6.5, 10% IPN
Resolution 1.59 Å R-free 0.211
4TQB The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；PEG 4000 12-20%, 100mM MES pH 6.5, 10% IPN
Resolution 1.59 Å R-free 0.211
4TQC The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1 34J (2S)-3-(4-amino-3-nitrophenyl)-2-{2-[(4P)-4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]hydrazin-1-yl}propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；PEG 4000 12-20%, 100mM MES pH 8.5, 10% IPN
Resolution 1.80 Å R-free 0.194
4TQC The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；PEG 4000 12-20%, 100mM MES pH 8.5, 10% IPN
Resolution 1.80 Å R-free 0.194
4UED Complex of human eIF4E with the 4E binding protein 4E-BP1 Deposited 2014-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–217（182 aa） Fragment：RESIDUES 36-217
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.03M EACH DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 0.1M BICINE/TRIZMA BASE PH 8.5, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD
Resolution 1.75 Å R-free 0.237
5EHC Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded 5NX 3-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-7-[(3-chlorophenyl)methyl]-6-oxidanylidene-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1???3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding
Resolution 2.40 Å R-free 0.264
5EI3 Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-10-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded 5O8 ~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-1,1,1-tris(fluoranyl)methanesulfonamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1???3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding
Resolution 1.71 Å R-free 0.187
5EIR Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-10-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded 5O8 ~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-1,1,1-tris(fluoranyl)methanesulfonamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1???3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding. Crystals replaced in to above conditions without (NH4)2SO4 prior to freezing.
Resolution 2.69 Å R-free 0.272
5EKV Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded 5PQ 3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1-3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding
Resolution 3.61 Å R-free 0.342
5EKV Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–217（217 aa）
Not recorded 5PQ 3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1-3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding
Resolution 3.61 Å R-free 0.342
5GW6 Water-Bridge Mediates Recognition of mRNA Cap in eIF4E Deposited 2016-09-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–217（195 aa）
Mutation：E105A, K106A, K108A GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；20% PEG 5000 MME, 100MM TRIS BIS PH 5.0, 0.05M AMMONIUM SULPHATE
Resolution 1.97 Å R-free 0.228
5T46 Crystal structure of the human eIF4E-eIF4G complex Deposited 2016-08-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.25；293 K；0.1 M Hepes pH 7.25, 25% w/v PEG 6000
Resolution 1.53 Å R-free 0.162
5T46 Crystal structure of the human eIF4E-eIF4G complex Deposited 2016-08-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–217（217 aa）
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.25；293 K；0.1 M Hepes pH 7.25, 25% w/v PEG 6000
Resolution 1.53 Å R-free 0.162
5ZJY Stapled-peptides tailored against initiation of translation Deposited 2018-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；30%(W/V) PEG 6000, 0.1M Na-Hepes pH6.5
Resolution 1.59 Å R-free 0.216
5ZJZ Stapled-peptides tailored against initiation of translation Deposited 2018-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；12.5%(w/v) PEG20000, 20%(w/v) PEG MME 550, 0.1M MES/imidazole pH 6.5
Resolution 1.67 Å R-free 0.212
5ZK5 Stapled-peptides tailored against initiation of translation Deposited 2018-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–217（190 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；30%(w/v) PEG6000, 0.1M Na-Hepes pH 6.5
Resolution 2.25 Å R-free 0.268
5ZK7 Stapled-peptides tailored against initiation of translation Deposited 2018-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 IOD IODIDE ION × 4 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.2M Potassium Iodide, 0.1M MES/Imidazole pH6.5, 25%(wv) PEG4000
Resolution 2.12 Å R-free 0.270
5ZK7 Stapled-peptides tailored against initiation of translation Deposited 2018-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 28–217（190 aa） Fragment：UNP residues 28-217
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 IOD IODIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.2M Potassium Iodide, 0.1M MES/Imidazole pH6.5, 25%(wv) PEG4000
Resolution 2.12 Å R-free 0.270
5ZK9 Stapled-peptides tailored against initiation of translation Deposited 2018-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–217（190 aa）
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；12.5% pEG1000 w/v, 12.5% PEG3350 w/v, 12.5% MPD w/v, 0.1M MES/imidazole pH 6.5
Resolution 1.76 Å R-free 0.211
5ZML Stapled-peptides tailored against initiation of translation Deposited 2018-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–217（191 aa）
Not recorded NO3 NITRATE ION × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；40%(v/v) Ethylene glycol, 20 %(w/v) PEG 8000, 0.3M Sodium nitrate, 0.3M Ammonium sulfate, 100mM Sodium HEPES/MOPS pH 7.5
Resolution 1.80 Å R-free 0.223
7D6Y eIF4E in Complex with a Disulphide-Free Autonomous VH Domain Deposited 2020-10-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；25% (w/v) PEG 6000, 0.01-02 M Ammonium Sulphate, 100mM Tris, pH 8.5
Resolution 1.67 Å R-free 0.206
7D8B Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways Deposited 2020-10-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.01M Tri-sodium citrate, 16% PEG 6000
Resolution 2.46 Å R-free 0.292
7D8B Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways Deposited 2020-10-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–217（217 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.01M Tri-sodium citrate, 16% PEG 6000
Resolution 2.46 Å R-free 0.292
7EZW Cyclic Peptide that Interacts with the eIF4E Capped-mRNA Binding Site Deposited 2021-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Potassium chloride 20% (w/v) PEG 3350
Resolution 2.35 Å R-free 0.248
7F07 Autonomous VH domain that interacts with eIF4E at the Capped mRNA Binding site. Deposited 2021-06-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M TRIS.HCl pH 8.5 25% (v/v) PEG 550 MME
Resolution 2.25 Å R-free 0.266
7MEU A biphenyl inhibitor of eIF4E targeting an internal binding site enables the design of cell-permeable PROTAC-degraders Deposited 2021-04-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–217（191 aa）
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 Z5D (2E)-2-{2-[4-([1,1'-biphenyl]-4-yl)-1,3-thiazol-2-yl]hydrazinylidene}-3-(2-nitrophenyl)propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；PEG 4000 10-20%, 100mM MES pH 6.5, 10% IPN
Resolution 1.91 Å R-free 0.219
7MEU A biphenyl inhibitor of eIF4E targeting an internal binding site enables the design of cell-permeable PROTAC-degraders Deposited 2021-04-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–217（191 aa）
Not recorded MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；PEG 4000 10-20%, 100mM MES pH 6.5, 10% IPN
Resolution 1.91 Å R-free 0.219
7XTP eIF4E in Complex with a Disulphide-Free Autonomous VH Domain Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa）
Not recorded MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Sodium HEPES pH7.5, 25% PEG 6000
Resolution 1.83 Å R-free 0.259
7XTP eIF4E in Complex with a Disulphide-Free Autonomous VH Domain Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–217（217 aa）
Not recorded MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Sodium HEPES pH7.5, 25% PEG 6000
Resolution 1.83 Å R-free 0.259
8QM4 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–217（182 aa）
Chain B 36–217（182 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 2 PGE TRIETHYLENE GLYCOL × 2 W5B 3-phenylphenol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；273 K；0.002M DTT, 40% PEG 400, 0.1M pH=7.5 HEPES/NaOH
Resolution 1.85 Å R-free 0.217
8QM5 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–217（182 aa）
Chain B 36–217（182 aa）
Not recorded W4U 1-(4-chlorophenyl)cyclopentane-1-carboxylic acid × 2 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.002M DTT 40% PEG 400 0.1M pH=7.5 HEPES/NaOH
Resolution 1.89 Å R-free 0.220
8QM6 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–217（182 aa）
Chain B 36–217（182 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 3 W2N (1~{S})-1-[4-(2-fluorophenyl)phenyl]ethanol × 2 W4B (1~{R})-1-[4-(2-fluorophenyl)phenyl]ethanol × 2 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.002M DTT 40% PEG 400 0.1M pH=8 Tris/HCl
Resolution 1.93 Å R-free 0.227
8QM7 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–217（182 aa）
Chain B 36–217（182 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 3 PGE TRIETHYLENE GLYCOL × 1 W5K (2~{R})-2-[(1~{R})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]propan-1-ol × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.002M DTT 38% PEG 400 0.1M pH=8 Tris/HCl
Resolution 2.19 Å R-free 0.240
8QM8 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–217（182 aa）
Chain B 36–217（182 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 6 PGE TRIETHYLENE GLYCOL × 1 W4K (2~{R})-2-[(1~{S})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]propan-1-ol × 2 DMS DIMETHYL SULFOXIDE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10% PEG 3350 0.1M pH=8 Bicine/NaOH
Resolution 1.58 Å R-free 0.202
8QM9 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–217（182 aa）
Chain B 36–217（182 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 4 DMS DIMETHYL SULFOXIDE × 2 W4K (2~{R})-2-[(1~{S})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]propan-1-ol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.002M DTT 38% PEG 400 0.1M pH=8 Tris/HCl
Resolution 1.97 Å R-free 0.272
8SX4 Crystal Structure of eIF4e in complex with Compound 7n Deposited 2023-05-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–217（190 aa）
Not recorded WXL [(~{Z})-4-[2-azanyl-7-[(5-chloranyl-1~{H}-indol-2-yl)methyl]-6-oxidanylidene-1~{H}-purin-9-yl]but-2-enyl]phosphonic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；16-26% Peg 3350, 0.1 M MES pH 6.0, 10% isopropanol and 2 mM CaCl2
Resolution 1.99 Å R-free 0.243
8SX4 Crystal Structure of eIF4e in complex with Compound 7n Deposited 2023-05-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–217（190 aa）
Not recorded M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；16-26% Peg 3350, 0.1 M MES pH 6.0, 10% isopropanol and 2 mM CaCl2
Resolution 1.99 Å R-free 0.243
9DON Crystal structure of eIF4e in complex with Compound 5-PA Deposited 2024-09-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–217（190 aa）
Not recorded M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；26% Peg 3350, 0.1 M MES pH 6.0, 10% isopropanol and 2 mM CaCl2
Resolution 2.09 Å R-free 0.247
9DON Crystal structure of eIF4e in complex with Compound 5-PA Deposited 2024-09-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–217（190 aa）
Not recorded A1A8P 2-[3-[[2-azanyl-7-[(5-chloranyl-1-benzofuran-2-yl)methyl]-6-oxidanylidene-1~{H}-purin-9-yl]methyl]phenyl]ethylphosphonic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；26% Peg 3350, 0.1 M MES pH 6.0, 10% isopropanol and 2 mM CaCl2
Resolution 2.09 Å R-free 0.247

44 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IF4E_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–217； UniProt 1–217

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1ipb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ipb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ipb
Deposition date deposition_date2001-05-08
Structure title titleCRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GPPPA
Keywords keywordsInitiation factor, Protein biosynthesis, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.57 Å
Radius of gyration Rg (electron density) rg_electron17.51 Å
Forward intensity I(0) i010330800.00
Molecular weight molecular_weight23045.0 kDa
Excluded volume excluded_volume28525 ų
Envelope volume envelope_volume34252 ų
Hydration-shell volume shell_volume16839 ų
Envelope diameter envelope_diameter76.9 Å
Shell Rg shell_rg23.45 Å
Envelope Rg envelope_rg18.30 Å
Shape Rg shape_rg17.48 Å
Total Rg total_rg18.54 Å
Total atoms total_atoms1623
Residues n_residues191
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax47.8 Å
Rg (real space) rg_real17.46 Å
Rg uncertainty (real space) rg_real_error0.05 Å
I(0) (real space) i0_real9.8230e+06
I(0) uncertainty (real space) i0_real_error8.9170e+04
Rg (reciprocal space) rg_reciprocal18.59 Å
I(0) (reciprocal space) i0_reciprocal10330000.0000
Solution quality estimate total_estimate0.6853
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.9 Å
Skewness Skewness skewness0.105
Kurtosis Kurtosis kurtosis-0.422
Angular range angular_range— – 0.4300 Å−1
Current regularization parameter α current_alpha2.0340
Highest regularization parameter α highest_alpha1907000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.004; Oscil: 0.986; Stabil: 0.988; Sysdev: 0.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ipba_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.86 — eIF4e-like
Superfamily Superfamily superfamilyd.86.1 — eIF4e-like
Family Family familyd.86.1.1 — Translation initiation factor eIF4e

CATH v4.4 (1 domains)

Domain ID domain_id1ipbA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology760 — RNA Cap, Translation Initiation Factor Eif4e
Homologous superfamily homologous superfamily10 — RNA Cap, Translation Initiation Factor Eif4e
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8. Citations (1)

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9. Files and Curves (10)