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5m81

Translation initiation factor 4E in complex with (SP)-iPr-m7GppSpG mRNA 5' cap analog

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Eukaryotic translation initiation factor 4E

Mus musculus

UniProt P63073

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ;[[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate ; × 1 GLYCEROL × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 ;[[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate ; × 1 GLYCEROL × 2 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 ;[[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate ; × 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 ;[[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate ; × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ej1 1ej1 1l8b 1l8b 5j5o 5j5o 5j5o 5j5o 5j5y 5j5y 5j5y 5j5y

74 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ej4 1ejh 1ejh 1ejh 1ejh 5bxv 5bxv

7 assemblies

View Construct and Data Evidence
UniProt name IF4E_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–190； UniProt 28–217 Author chain B； PDBConstruct 1–190； UniProt 28–217 Author chain C； PDBConstruct 1–190； UniProt 28–217 Author chain D； PDBConstruct 1–190； UniProt 28–217

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id5m81
Deposition date deposition_date2016-10-28
Structure title titleTranslation initiation factor 4E in complex with (SP)-iPr-m7GppSpG mRNA 5' cap analog
Keywords keywords;Protein-ligand complex, translation initiation factor, eIF4E, iPr-m7GppSpG, phosphorothioate, mRNA 5' cap analog, translation ;; TRANSLATION
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5m81__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5m81__assembly_1__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5m81__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）17.64 Å
Rg (electron density)16.47 Å
Total Rg17.56 Å
Atom count1579
Residues187
Excluded volume27794 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5m81__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5m81__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5m81__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5m81__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5m81a_
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
Domain ID domain_idd5m81b_
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
Domain ID domain_idd5m81c_
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
Domain ID domain_idd5m81d_
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 (4 domains)

Domain ID domain_id5m81A00
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
Domain ID domain_id5m81B00
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
Domain ID domain_id5m81C00
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
Domain ID domain_id5m81D00
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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7. Citations (1)