SAXSdb — 4u1d

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

Eukaryotic translation initiation factor 3 subunit A

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 C； UniProt 1–494	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；292 K；PEG 3350, KSCN, Bis-Tris-propane	Resolution 3.30 Å R-free 0.204
2	Protein monomer Monomer Protein × 1 PDB declaration: Monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–494	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；292 K；PEG 3350, KSCN, Bis-Tris-propane	Resolution 3.30 Å R-free 0.204
3	Protein monomer Monomer Protein × 1 PDB declaration: Monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–494	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；292 K；PEG 3350, KSCN, Bis-Tris-propane	Resolution 3.30 Å R-free 0.204

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 4U1D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JAP Structure of a partial yeast 48S preinitiation complex in closed conformation Deposited 2015-06-18	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 o 1–495（495 aa）	Not recorded	MG MAGNESIUM ION × 81 ZN ZINC ION × 4 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT；pH 6.5；20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT cryo-EM vitrification conditions Blot for 2.5 to 3 seconds before plunging；120 K；Cryogen ETHANE；Blot for 2.5 to 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).	Resolution 4.90 Å
4K51 Crystal Structure of the PCI domain of eIF3a Deposited 2013-04-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 276–494（219 aa） Fragment：PCI, UNP residues 276-494	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG, buffer, salt, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.65 Å R-free 0.286
4K51 Crystal Structure of the PCI domain of eIF3a Deposited 2013-04-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 276–494（219 aa） Fragment：PCI, UNP residues 276-494	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG, buffer, salt, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.65 Å R-free 0.286
4U1C Crystal structure of the eIF3a/eIF3c PCI-domain heterodimer Deposited 2014-07-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: Dimeric	Chain A 225–495（271 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；PEG 6000, KSCN, Bis-Tris-propane	Resolution 3.50 Å R-free 0.293
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 o 1–964（964 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 o 1–964（964 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
6GSM Structure of a partial yeast 48S preinitiation complex in open conformation. Deposited 2018-06-14	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 o 5–492（488 aa）	Not recorded	7NO [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] (2~{S})-2-azanyl-4-methylsulfanyl-butanoate × 1 MG MAGNESIUM ION × 82 ZN ZINC ION × 4 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.15 Å
6GSN Structure of a partial yeast 48S preinitiation complex in closed conformation Deposited 2018-06-14	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 o 5–492（488 aa）	Not recorded	MG MAGNESIUM ION × 81 ZN ZINC ION × 4 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.75 Å
6ZCE Structure of a yeast ABCE1-bound 43S pre-initiation complex Deposited 2020-06-10	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: 45-meric	Chain o 1–964（964 aa）	Not recorded	ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 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 5.30 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 o 1–964（964 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
8CAH Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex Deposited 2023-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 48-meric	Chain o 1–964（964 aa）	Not recorded	MG MAGNESIUM ION × 80 ZN ZINC ION × 2 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8CAS Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial) Deposited 2023-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain o 1–964（964 aa）	Not recorded	ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 2 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8S8E Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.1) 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 × 40 PDB declaration: 43-meric	Chain o 1–964（964 aa）	Not recorded	MG MAGNESIUM ION × 116 ZN ZINC ION × 3 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MET METHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.85 Å

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EIF3A_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–497； UniProt 1–494 Author chain B； PDBConstruct 4–497； UniProt 1–494 Author chain C； PDBConstruct 4–497； UniProt 1–494

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	4u1d
Deposition date deposition_date	2014-07-15
Structure title title	Structure of the PCI domain of translation initiation factor eIF3a
Keywords keywords	translation initiation, eIF3 complex, PCI domain, 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	37.87 Å
Radius of gyration Rg (electron density) rg_electron	37.38 Å
Forward intensity I(0) i0	340748000.00
Molecular weight molecular_weight	155890.0 kDa
Excluded volume excluded_volume	197930 Å³
Envelope volume envelope_volume	263810 Å³
Hydration-shell volume shell_volume	58609 Å³
Envelope diameter envelope_diameter	134.1 Å
Shell Rg shell_rg	43.65 Å
Envelope Rg envelope_rg	37.03 Å
Shape Rg shape_rg	37.37 Å
Total Rg total_rg	37.85 Å
Total atoms total_atoms	11013
Residues n_residues	1352
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	122.2 Å
Rg (real space) rg_real	37.72 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	3.4070e+08
I(0) uncertainty (real space) i0_real_error	5.1880e+06
Rg (reciprocal space) rg_reciprocal	37.82 Å
I(0) (reciprocal space) i0_reciprocal	340800000.0000
Solution quality estimate total_estimate	0.8951
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	46.5 Å
Skewness Skewness skewness	0.209
Kurtosis Kurtosis kurtosis	-0.442
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	40040000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.934

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	242.530 Å
Unit-cell length b length_b	158.270 Å
Unit-cell length c length_c	93.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	39.568 Å
R factor r_factor	0.1719
R_work r_work	0.1703
R_free r_free	0.2037

Description description	Eukaryotic translation initiation factor 3 subunit A
Molecular weight formula_weight	57012.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,B,A
Atom count atom_count	11013

Structure of the PCI domain of translation initiation factor eIF3a

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

Eukaryotic translation initiation factor 3 subunit A

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/u1/4u1d/4u1d.fit
pddf	/app/data/pr_computation/u1/4u1d/4u1d.pr.out
profile	/app/data/saxs_computation/u1/4u1d/4u1d.dat