SAXSdb — 2ful

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 241–405	Fragment：residues 236-412	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；2.8M (NH4)2SO4, 0.1M MES pH6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.205
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 241–405	Fragment：residues 236-412	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；2.8M (NH4)2SO4, 0.1M MES pH6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.205
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 241–405	Fragment：residues 236-412	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；2.8M (NH4)2SO4, 0.1M MES pH6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.205
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 241–405	Fragment：residues 236-412	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；2.8M (NH4)2SO4, 0.1M MES pH6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.205
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 241–405	Fragment：residues 236-412	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；2.8M (NH4)2SO4, 0.1M MES pH6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.205
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 241–405	Fragment：residues 236-412	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；2.8M (NH4)2SO4, 0.1M MES pH6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.205

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 2FUL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6FYX Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1) Deposited 2018-03-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric	Chain m 1–405（405 aa）	Not recorded	MG MAGNESIUM ION × 117 ZN ZINC ION × 5 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6FYY Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2) Deposited 2018-03-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric	Chain m 1–405（405 aa）	Not recorded	MG MAGNESIUM ION × 117 ZN ZINC ION × 5 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.02 Å
6ZU9 Structure of a yeast ABCE1-bound 48S initiation complex Deposited 2020-07-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric	Chain m 1–405（405 aa）	Not recorded	MG MAGNESIUM ION × 4 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.20 Å
8S8J Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF5) Deposited 2024-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric	Chain m 1–405（405 aa）	Not recorded	MG MAGNESIUM ION × 115 ZN ZINC ION × 4 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
9F79 Crystal structure of the S. cerevisiae eIF2beta N-terminal tail bound to the C-terminal domain of eIF5 Deposited 2024-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 201–405（205 aa） Chain B 201–405（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；283 K；0.4 M (NH4)2SO4, 0.08 M Li2SO4	Resolution 2.00 Å R-free 0.228

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IF5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–170； UniProt 241–405 Author chain B； PDBConstruct 6–170； UniProt 241–405 Author chain C； PDBConstruct 6–170； UniProt 241–405 Author chain D； PDBConstruct 6–170； UniProt 241–405 Author chain E； PDBConstruct 6–170； UniProt 241–405 Author chain F； PDBConstruct 6–170； UniProt 241–405

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	2ful
Deposition date deposition_date	2006-01-27
Structure title title	Crystal Structure of the C-terminal Domain of S. cerevisiae eIF5
Keywords keywords	atypical HEAT motif, 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	41.38 Å
Radius of gyration Rg (electron density) rg_electron	41.66 Å
Forward intensity I(0) i0	185099000.00
Molecular weight molecular_weight	112840.0 kDa
Excluded volume excluded_volume	141940 Å³
Envelope volume envelope_volume	196970 Å³
Hydration-shell volume shell_volume	41669 Å³
Envelope diameter envelope_diameter	164.3 Å
Shell Rg shell_rg	43.47 Å
Envelope Rg envelope_rg	41.80 Å
Shape Rg shape_rg	41.66 Å
Total Rg total_rg	41.76 Å
Total atoms total_atoms	7929
Residues n_residues	970
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	153.9 Å
Rg (real space) rg_real	41.69 Å
Rg uncertainty (real space) rg_real_error	2.20 Å
I(0) (real space) i0_real	1.8510e+08
I(0) uncertainty (real space) i0_real_error	3.8070e+06
Rg (reciprocal space) rg_reciprocal	41.38 Å
I(0) (reciprocal space) i0_reciprocal	185000000.0000
Solution quality estimate total_estimate	0.8152
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.5 Å
Skewness Skewness skewness	0.483
Kurtosis Kurtosis kurtosis	-0.443
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15220000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.635; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.706; Smooth: 0.981

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Eukaryotic translation initiation factor 5
Molecular weight formula_weight	20412.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9151

GSPEFVNSELTQLDEYGEWILEQAGEDKENLPSDVELYKKAAELDVLNDPKIGCVLAQCLFDEDIVNEIAEHNAFFTKILVTPEYEKNFMGGIERFLGLEHKDLIPLLPKILVQLYNNDIISEEEIMRFGTKSSKKFVPKEVSKKVRRAAKPFITWLETAESDDDEEDDELERPHRD

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	916

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2fulA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	2fulB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	2fulC01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	2fulD01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	2fulE01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	2fulF01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

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8. Citations (1)

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Unit-cell length a length_a	44.849 Å
Unit-cell length b length_b	64.536 Å
Unit-cell length c length_c	108.916 Å
Unit-cell angle α angle_alpha	88.60 °
Unit-cell angle β angle_beta	86.57 °
Unit-cell angle γ angle_gamma	74.93 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.1770
R_free r_free	0.2050

fit	/app/data/saxs_computation/fu/2ful/2ful.fit
pddf	/app/data/pr_computation/fu/2ful/2ful.pr.out
profile	/app/data/saxs_computation/fu/2ful/2ful.dat

Crystal Structure of the C-terminal Domain of S. cerevisiae 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

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