SAXSdb — 5nvm

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

Eukaryotic translation initiation factor 4E type 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	GRB10-interacting GYF protein 2 × 1 （Q6Y7W6） PHOSPHATE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	GRB10-interacting GYF protein 2 × 1 （Q6Y7W6） PHOSPHATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF4E2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–189； UniProt 52–234 Author chain C； PDBConstruct 7–189； UniProt 52–234

GRB10-interacting GYF protein 2

Homo sapiens

UniProt Q6Y7W6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Eukaryotic translation initiation factor 4E type 2 × 1 （O60573） PHOSPHATE ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Eukaryotic translation initiation factor 4E type 2 × 1 （O60573） PHOSPHATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GGYF2_HUMAN
Isoform	Q6Y7W6-3
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–42； UniProt 35–72 Author chain D； PDBConstruct 5–42； UniProt 35–72

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	5nvm
Deposition date deposition_date	2017-05-04
Structure title title	Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences
Keywords keywords	translational regulation, cap-binding protein, 4EHP-binding protein, GRB10-interacting GYF protein 2, 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.

5nvm__assembly_1__model_1

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

Download this curve (.dat)

5nvm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nvm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.46 Å
Rg (electron density)	17.14 Å
Total Rg	18.24 Å
Atom count	3487
Residues	213
Excluded volume	31279 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nvm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5nvm__assembly_2__model_1`	dimeric （2）	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)

Entity 1 Entity 1 polymer

Description description	Eukaryotic translation initiation factor 4E type 2
Molecular weight formula_weight	21979.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6861

GPHMLEAEHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNTIMEYKTHTDSIKMPGRLGPQRLLF

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	GRB10-interacting GYF protein 2
Molecular weight formula_weight	5018.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GPHMKYKLADYRYGREEMLALFLKDNKIPSDLLDKEFLPILQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	130

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5nvma1
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

Domain ID domain_id	d5nvma2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5nvmc1
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

Domain ID domain_id	d5nvmc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5nvmA01
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	5nvmC01
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	152.210 Å
Unit-cell length b length_b	98.590 Å
Unit-cell length c length_c	39.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	44.613 Å
R factor r_factor	0.2001
R_work r_work	0.1984
R_free r_free	0.2326

Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences

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

Eukaryotic translation initiation factor 4E type 2

State in the Current Structure

Other States of the Same Protein in the Database

GRB10-interacting GYF protein 2

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

5nvm__assembly_1__model_1

5nvm__assembly_1__model_1 | I(q)

5nvm__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences

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

Eukaryotic translation initiation factor 4E type 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GRB10-interacting GYF protein 2

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

5nvm__assembly_1__model_1

5nvm__assembly_1__model_1 | I(q)

5nvm__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)