SAXSdb — 6ylt

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

Eukaryotic translation initiation factor 4E

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;[[(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 ; × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;[[(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 ; × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	;[[(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 ; × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	;[[(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 ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF4E_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–191； UniProt 28–217 Author chain B； PDBConstruct 2–191； UniProt 28–217 Author chain C； PDBConstruct 2–191； UniProt 28–217 Author chain D； PDBConstruct 2–191； 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_id	6ylt
Deposition date deposition_date	2020-04-07
Structure title title	Translation initiation factor 4E in complex with 3-MeBn7GpppG mRNA 5' cap analog
Keywords keywords	cap analog, translation initiation factor, 3-MeBn7GpppG, protein-ligand complex, eIF4E, TRANSLATION; TRANSLATION
Experimental Method method	X-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.

6ylt__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6ylt__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ylt__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	17.16 Å
Rg (electron density)	15.85 Å
Total Rg	16.93 Å
Atom count	1409
Residues	181
Excluded volume	24447 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ylt__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ylt__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6ylt__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6ylt__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 (3)

Entity 1 Entity 1 polymer

Description description	Eukaryotic translation initiation factor 4E
Molecular weight formula_weight	22276.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6261

MVANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENRDAVTHIGRVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRFVV

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;[[(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 ;
Molecular weight formula_weight	893.6 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6ylta_
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.86.1.1 — Translation initiation factor eIF4e

Domain ID domain_id	d6yltb_
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.86.1.1 — Translation initiation factor eIF4e

Domain ID domain_id	d6yltc_
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.86.1.1 — Translation initiation factor eIF4e

Domain ID domain_id	d6yltd_
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.86.1.1 — Translation initiation factor eIF4e

CATH v4.4 (4 domains)

Domain ID domain_id	6yltA00
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

Domain ID domain_id	6yltB00
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

Domain ID domain_id	6yltC00
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

Domain ID domain_id	6yltD00
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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Unit-cell length a length_a	38.300 Å
Unit-cell length b length_b	38.330 Å
Unit-cell length c length_c	148.760 Å
Unit-cell angle α angle_alpha	83.99 °
Unit-cell angle β angle_beta	87.78 °
Unit-cell angle γ angle_gamma	76.81 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.670 Å
Low-resolution limit resolution_low	49.310 Å
R factor r_factor	0.2021
R_work r_work	0.2003
R_free r_free	0.2462

Translation initiation factor 4E in complex with 3-MeBn7GpppG mRNA 5' cap analog

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

Eukaryotic translation initiation factor 4E

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ylt__assembly_3__model_1

6ylt__assembly_3__model_1 | I(q)

6ylt__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Translation initiation factor 4E in complex with 3-MeBn7GpppG mRNA 5' cap analog

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

Eukaryotic translation initiation factor 4E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ylt__assembly_3__model_1

6ylt__assembly_3__model_1 | I(q)

6ylt__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)