SAXSdb — 9f79

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

Eukaryotic translation initiation factor 5

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Eukaryotic translation initiation factor 2 subunit beta × 2 （P09064） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–210； UniProt 201–405 Author chain B； PDBConstruct 6–210； UniProt 201–405

Eukaryotic translation initiation factor 2 subunit beta

Saccharomyces cerevisiae

UniProt P09064

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Eukaryotic translation initiation factor 5 × 4 （P38431） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF2B_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 6–73； UniProt 39–106

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	9f79
Deposition date deposition_date	2024-05-03
Structure title title	Crystal structure of the S. cerevisiae eIF2beta N-terminal tail bound to the C-terminal domain of eIF5
Keywords keywords	Translation, Eukaryotic translation initiation factor, Complex, eIF5, W2 domain, eIF2 beta; 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.

9f79__assembly_1__model_1

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

Download this curve (.dat)

9f79__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9f79__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.90 Å
Rg (electron density)	36.47 Å
Total Rg	36.72 Å
Atom count	7112
Residues	894
Excluded volume	127250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9f79__assembly_1__model_1`	hexameric （6）	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 5
Molecular weight formula_weight	23934.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3824

GPLGSELSRQIKAAASTLEDIEVKDDEWAVDMSEEAIRARAKELEVNSELTQLDEYGEWILEQAGEDKENLPSDVELYKKAAELDVLNDPKIGCVLAQCLFDEDIVNEIAEHNAFFTKILVTPEYEKNFMGGIERFLGLEHKDLIPLLPKILVQLYNNDIISEEEIMRFGTKSSKKFVPKEVSKKVRRAAKPFITWLETAESDDDEEDDE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Eukaryotic translation initiation factor 2 subunit beta
Molecular weight formula_weight	7681.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPLGSGSGDDLFAGLKKKKKKSKSVSADAEAEKEPTDDIAEALGELSLKKKKKKTKDSSVDAFEKELAKAGLD

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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Unit-cell length a length_a	74.180 Å
Unit-cell length b length_b	74.180 Å
Unit-cell length c length_c	224.420 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 1 2
Space-group number int_tables_number	153
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	37.400 Å
R factor r_factor	0.2077
R_work r_work	0.2067
R_free r_free	0.2277

Crystal structure of the S. cerevisiae eIF2beta N-terminal tail bound to the C-terminal domain of eIF5

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

Eukaryotic translation initiation factor 5

State in the Current Structure

Other States of the Same Protein in the Database

Eukaryotic translation initiation factor 2 subunit beta

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

9f79__assembly_1__model_1

9f79__assembly_1__model_1 | I(q)

9f79__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of the S. cerevisiae eIF2beta N-terminal tail bound to the C-terminal domain of eIF5

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

Eukaryotic translation initiation factor 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Eukaryotic translation initiation factor 2 subunit beta

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

9f79__assembly_1__model_1

9f79__assembly_1__model_1 | I(q)

9f79__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)