SAXSdb — 3m94

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Translation initiation factor 4E

Ascaris suum

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 49–236	Fragment：UNP residues 49-236	Eukaryotic translation initiation factor 4E-binding protein 1 × 1 （Q13541） M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1 ACE ACETYL GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；20% MMG PEG 2000, 0.2 M (NH4)2SO4 and 100 mM Na-Critate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.05 Å R-free 0.244

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 3M94	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3M93 Complex crystal structure of Ascaris suum eIF4E-3 with m7G cap Deposited 2010-03-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 49–236（188 aa） Fragment：UNP residues 49-236	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；20% MMG PEG 2000, 0.2 M (NH4)2SO4, and 100 mM Na-Critate, pH 5.6, VAPOR DIFFUSION, temperature 277K	Resolution 2.90 Å R-free 0.294

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6PKX2_ASCSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–189； UniProt 49–236

Eukaryotic translation initiation factor 4E-binding protein 1

OrganismNot specified

UniProt Q13541

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 51–67	Fragment：UNP residues 51-67	Translation initiation factor 4E × 1 （Q6PKX2） M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1 ACE ACETYL GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；20% MMG PEG 2000, 0.2 M (NH4)2SO4 and 100 mM Na-Critate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.05 Å R-free 0.244

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 3M94	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WKW Crystal structure of the ternary complex of eIF4E-m7GpppA-4EBP1 peptide Deposited 2004-06-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 47–66（20 aa） Fragment：RESIDUES 47-66	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
2JGB Structure of human eIF4E homologous protein 4EHP with m7GTP Deposited 2007-02-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–66（17 aa） Fragment：RESIDUES 50-66	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；20% PEG-3000, 0.1M SODIUM CITRATE PH 5.5 WITH 1MM M7GTP IN THE DROP	Resolution 1.70 Å R-free 0.242
2JGC Structure of the human eIF4E homologous protein, 4EHP without ligand bound Deposited 2007-02-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–66（17 aa） Fragment：RESIDUES 50-66	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；20% PEG-3000, 0.1M SODIUM CITRATE PH 5.5	Resolution 2.40 Å R-free 0.249
2V8W Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–63（14 aa） Fragment：PHAS-I4E-BP1 BINDING PEPTIDE, RESIDUES 50-63	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 50–63（14 aa） Fragment：PHAS-I4E-BP1 BINDING PEPTIDE, RESIDUES 50-63	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–63（14 aa） Fragment：PHAS-I4E-BP1 BINDING PEPTIDE, RESIDUES 50-63	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 50–63（14 aa） Fragment：PHAS-I4E-BP1 BINDING PEPTIDE, RESIDUES 50-63	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–63（14 aa） Fragment：PHAS-I4E-BP1 BINDING PEPTIDE, RESIDUES 50-63	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 50–63（14 aa） Fragment：PHAS-I4E-BP1 BINDING PEPTIDE, RESIDUES 50-63	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
3HXG Crystal structure of Schistsome eIF4E complexed with m7GpppA and 4E-BP Deposited 2009-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 51–67（17 aa） Fragment：residues 51-67	Not recorded	GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；279 K；100mM pH 6.5 Mops, 20% PEG4K, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.10 Å R-free 0.269
3HXI Crystal structure of Schistosome eIF4E complexed with m7GpppG and 4E-BP Deposited 2009-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 51–67（17 aa） Fragment：residues 51-67	Not recorded	GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100mM pH 6.5 Mops, 20% PEG4K, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.272
3M93 Complex crystal structure of Ascaris suum eIF4E-3 with m7G cap Deposited 2010-03-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 51–67（17 aa） Fragment：UNP residues 51-67	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；20% MMG PEG 2000, 0.2 M (NH4)2SO4, and 100 mM Na-Critate, pH 5.6, VAPOR DIFFUSION, temperature 277K	Resolution 2.90 Å R-free 0.294
3U7X Crystal structure of the human eIF4E-4EBP1 peptide complex without cap Deposited 2011-10-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 47–66（20 aa） Fragment：UNP residues 46-66	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 47–66（20 aa） Fragment：UNP residues 46-66	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 C 47–66（20 aa） Fragment：UNP residues 46-66 Chain D 47–66（20 aa） Fragment：UNP residues 46-66	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
4UED Complex of human eIF4E with the 4E binding protein 4E-BP1 Deposited 2014-12-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–83（34 aa） Fragment：RESIDUES 50-83	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
5BXV eIF4E complex Deposited 2015-06-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 43–84（42 aa） Fragment：unp residues 50-84	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；298 K；0.1 M Tris-HCl, and 22 % polyethylene glycol 4000	Resolution 2.10 Å R-free 0.195
5BXV eIF4E complex Deposited 2015-06-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 43–84（42 aa） Fragment：unp residues 50-84	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；298 K；0.1 M Tris-HCl, and 22 % polyethylene glycol 4000	Resolution 2.10 Å R-free 0.195
5EKV Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-11-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 51–64（14 aa） Fragment：eIF4E binding sequence, UNP residues 51-64	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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 51–64（14 aa） Fragment：eIF4E binding sequence, UNP residues 51-64	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
5NVN Crystal structure of the human 4EHP-4E-BP1 complex Deposited 2017-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–83（34 aa）	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate pH 4.6 1.7 M sodium formate	Resolution 1.90 Å R-free 0.251
5NVN Crystal structure of the human 4EHP-4E-BP1 complex Deposited 2017-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 50–83（34 aa）	Not recorded	FMT FORMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate pH 4.6 1.7 M sodium formate	Resolution 1.90 Å R-free 0.251
5WBJ Crystal structure of the arabidopsis thaliana Raptor in complex with the TOS peptide of human 4EBP1 Deposited 2017-06-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 99–118（20 aa） Fragment：residues 99-118	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；tacsimate	Resolution 3.00 Å R-free 0.270
6BCU Cryo-EM structure of the activated RHEB-mTORC1 refined to 3.4 angstrom Deposited 2017-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain X 1–118（118 aa） Chain Z 1–118（118 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 6 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6BCX mTORC1 structure refined to 3.0 angstroms Deposited 2017-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain X 1–118（118 aa） Chain Z 1–118（118 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
8RCH CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, overall refinement Deposited 2023-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain X 1–118（118 aa） Chain Z 1–118（118 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8RCK CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, Focused on one protomer copy. Deposited 2023-12-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 1–118（118 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8RCN CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, Focused region of mTOR and RAPTOR on one protomer copy. Deposited 2023-12-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain X 1–118（118 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9ED4 A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane Deposited 2024-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain K 1–118（118 aa） Chain T 1–118（118 aa）	Not recorded	GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 2 MG MAGNESIUM ION × 8 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 IHP INOSITOL HEXAKISPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å

21 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	4EBP1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–17； UniProt 51–67

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3m94
Deposition date deposition_date	2010-03-19
Structure title title	Complex crystal structure of Ascaris suum eIF4E-3 with m2,2,7G cap
Keywords keywords	eIF4E, Berkeley Structural Genomics Center, BSGC, TRANSLATION; TRANSLATION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	17.52 Å
Radius of gyration Rg (electron density) rg_electron	16.10 Å
Forward intensity I(0) i0	9432630.00
Molecular weight molecular_weight	22591.0 kDa
Excluded volume excluded_volume	28212 Å³
Envelope volume envelope_volume	32345 Å³
Hydration-shell volume shell_volume	16567 Å³
Envelope diameter envelope_diameter	59.3 Å
Shell Rg shell_rg	22.57 Å
Envelope Rg envelope_rg	16.51 Å
Shape Rg shape_rg	16.05 Å
Total Rg total_rg	17.32 Å
Total atoms total_atoms	1592
Residues n_residues	193
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	57.5 Å
Rg (real space) rg_real	17.38 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	9.4330e+06
I(0) uncertainty (real space) i0_real_error	9.9310e+04
Rg (reciprocal space) rg_reciprocal	17.40 Å
I(0) (reciprocal space) i0_reciprocal	9433000.0000
Solution quality estimate total_estimate	0.7923
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.090
Kurtosis Kurtosis kurtosis	-0.346
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2664000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Translation initiation factor 4E
Molecular weight formula_weight	22169.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1631

MRHPLQCHWALWYLKADRSKDWEDCLKQVAVFDTVEDFWSLYNHIQAASGLTWGSDYYLFKEGIKPMWEDENNVKGGRWLVVVDKQKRAQLLDHYWLELLMAIIGEQFEDNGEYICGAVVNVRQKGDKVSLWTRDSLKDDVNLRIGQILKAKLEIPDTEPIRYEVHKDSSVRTGSMVKPRIVIPSKDNR

来源 Source

来源生物 organism	Ascaris suum
通用名 common_name	Pig roundworm
NCBI Class编号 ncbi_taxonomy_id	6253
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Eukaryotic translation initiation factor 4E-binding protein 1
Molecular weight formula_weight	2144.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

RIIYDRKFLMECRNSPV

Entity 3 Entity 3 non-polymer

Description description	;N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) ;
Molecular weight formula_weight	487.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ACETYL GROUP
Molecular weight formula_weight	44.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	39

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3m94a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.86 — eIF4e-like
Superfamily Superfamily superfamily	d.86.1 — eIF4e-like
Family Family family	d.86.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3m94A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	760 — RNA Cap, Translation Initiation Factor Eif4e
Homologous superfamily homologous superfamily	10 — RNA Cap, Translation Initiation Factor Eif4e

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8. Citations (1)

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Unit-cell length a length_a	104.977 Å
Unit-cell length b length_b	104.977 Å
Unit-cell length c length_c	46.906 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	19.160 Å
R factor r_factor	0.2077
R_work r_work	0.2036
R_free r_free	0.2443

fit	/app/data/saxs_computation/m9/3m94/3m94.fit
pddf	/app/data/pr_computation/m9/3m94/3m94.pr.out
profile	/app/data/saxs_computation/m9/3m94/3m94.dat

Complex crystal structure of Ascaris suum eIF4E-3 with m2,2,7G cap

1. Protein Identity and Related Structures Protein Identity & Related Structures

Translation initiation factor 4E

State in the Current Structure

Other States of the Same Protein in the Database

Eukaryotic translation initiation factor 4E-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)