SAXSdb — 4u1f

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

Eukaryotic translation initiation factor 3 subunit B

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 172–665 Chain B； UniProt 172–665	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；292 K；PEG MME 5000, potassium thiocyanate, CHES	Resolution 2.20 Å R-free 0.226

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 4U1F	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 mutation/modification 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 r 704–734（31 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
3NS5 Crystal structure of the RNA recognition motif of yeast eIF3b residues 76-161 Deposited 2010-07-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 76–161（86 aa） Fragment：residues 76-161	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；33% PEG4000 and 0.1 M Na-citrate (pH 5.6) in a sitting drop plate at 20 degrees. 1uL of protein at the concentration of 17 mg/mL was mixed with 1 uL of reservoir, VAPOR DIFFUSION, SITTING DROP	Resolution 2.60 Å R-free 0.273
3NS5 Crystal structure of the RNA recognition motif of yeast eIF3b residues 76-161 Deposited 2010-07-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 76–161（86 aa） Fragment：residues 76-161	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；33% PEG4000 and 0.1 M Na-citrate (pH 5.6) in a sitting drop plate at 20 degrees. 1uL of protein at the concentration of 17 mg/mL was mixed with 1 uL of reservoir, VAPOR DIFFUSION, SITTING DROP	Resolution 2.60 Å R-free 0.273
3NS6 Crystal structure of hte RNA recognition motif of yeast eIF3b residues 76-170 Deposited 2010-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 76–170（95 aa） Fragment：residues 76-170	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；30% PEG4000, 200 mM Li2SO4 and 100 mM Hepes pH 8. The crystals were grown in a sitting drop at 20 degrees by mixing 1uL of protein (11 mg/mL) with 1uL of reservoir, VAPOR DIFFUSION, SITTING DROP	Resolution 1.25 Å R-free 0.168
3NS6 Crystal structure of hte RNA recognition motif of yeast eIF3b residues 76-170 Deposited 2010-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 76–170（95 aa） Fragment：residues 76-170	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；30% PEG4000, 200 mM Li2SO4 and 100 mM Hepes pH 8. The crystals were grown in a sitting drop at 20 degrees by mixing 1uL of protein (11 mg/mL) with 1uL of reservoir, VAPOR DIFFUSION, SITTING DROP	Resolution 1.25 Å R-free 0.168
3NS6 Crystal structure of hte RNA recognition motif of yeast eIF3b residues 76-170 Deposited 2010-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 76–170（95 aa） Fragment：residues 76-170 Chain B 76–170（95 aa） Fragment：residues 76-170	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；30% PEG4000, 200 mM Li2SO4 and 100 mM Hepes pH 8. The crystals were grown in a sitting drop at 20 degrees by mixing 1uL of protein (11 mg/mL) with 1uL of reservoir, VAPOR DIFFUSION, SITTING DROP	Resolution 1.25 Å R-free 0.168
3ZWL Structure of eukaryotic translation initiation factor eIF3i complex with eIF3b C-terminus (655-700) Deposited 2011-08-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 693–739（47 aa） Fragment：RESIDUES 693-739	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.8；0.1 M TRIS PH 8.8, 0.1 M LI2SO4, 30% PEG4000, 8% DIAMINOPENTANE	Resolution 2.20 Å R-free 0.247
3ZWL Structure of eukaryotic translation initiation factor eIF3i complex with eIF3b C-terminus (655-700) Deposited 2011-08-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 693–739（47 aa） Fragment：RESIDUES 693-739	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.8；0.1 M TRIS PH 8.8, 0.1 M LI2SO4, 30% PEG4000, 8% DIAMINOPENTANE	Resolution 2.20 Å R-free 0.247
4U1E Crystal structure of the eIF3b-CTD/eIF3i/eIF3g-NTD translation initiation complex Deposited 2014-07-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric	Chain B 694–737（44 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；292 K；PEG 20000, PEG MME 550, imidazole, MES	Resolution 2.00 Å R-free 0.216
6FYX Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1) Deposited 2018-03-12	Different construct Different mutation/modification 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 p 1–763（763 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 mutation/modification 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 p 1–763（763 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 mutation/modification 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 p 77–737（661 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 mutation/modification 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 p 72–737（666 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 mutation/modification 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 p 1–763（763 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 mutation/modification 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 p 1–763（763 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

11 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EIF3B_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–497； UniProt 172–665 Author chain B； PDBConstruct 4–497； UniProt 172–665

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	4u1f
Deposition date deposition_date	2014-07-15
Structure title title	Crystal structure of middle domain of eukaryotic translation initiation factor eIF3b
Keywords keywords	translation initiation, eIF3 complex, beta-propeller, 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	36.80 Å
Radius of gyration Rg (electron density) rg_electron	36.33 Å
Forward intensity I(0) i0	179385000.00
Molecular weight molecular_weight	108640.0 kDa
Excluded volume excluded_volume	136110 Å³
Envelope volume envelope_volume	187880 Å³
Hydration-shell volume shell_volume	43368 Å³
Envelope diameter envelope_diameter	123.3 Å
Shell Rg shell_rg	42.49 Å
Envelope Rg envelope_rg	35.48 Å
Shape Rg shape_rg	36.27 Å
Total Rg total_rg	36.98 Å
Total atoms total_atoms	7685
Residues n_residues	949
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	118.7 Å
Rg (real space) rg_real	36.83 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	1.7940e+08
I(0) uncertainty (real space) i0_real_error	3.0780e+06
Rg (reciprocal space) rg_reciprocal	36.82 Å
I(0) (reciprocal space) i0_reciprocal	179400000.0000
Solution quality estimate total_estimate	0.8941
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.6 Å
Skewness Skewness skewness	0.286
Kurtosis Kurtosis kurtosis	-0.615
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12930000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.914

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Eukaryotic translation initiation factor 3 subunit B
Molecular weight formula_weight	56936.0 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	7892

SNADTEFREPDMPTFVPSSSLKSWLMDDKVRDQFVLQDDVKTSVFWNSMFNEEDSLVESRENWSTNYVRFSPKGTYLFSYHQQGVTAWGGPNFDRLRRFYHPDVRNSSVSPNEKYLVTFSTEPIIVEEDNEFSPFTKKNEGHQLCIWDIASGLLMATFPVIKSPYLKWPLVRWSYNDKYCARMVGDSLIVHDATKNFMPLEAKALKPSGIRDFSFAPEGVKLQPFRNGDEPSVLLAYWTPETNNSACTATIAEVPRGRVLKTVNLVQVSNVTLHWQNQAEFLCFNVERHTKSGKTQFSNLQICRLTERDIPVEKVELKDSVFEFGWEPHGNRFVTISVHEVADMNYAIPANTIRFYAPETKEKTDVIKRWSLVKEIPKTFANTVSWSPAGRFVVVGALVGPNMRRSDLQFYDMDYPGEKNINDNNDVSASLKDVAHPTYSAATNITWDPSGRYVTAWSSSLKHKVEHGYKIFNIAGNLVKEDIIAGFKNFAWRPRPA

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	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	207

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8. Citations (1)

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Unit-cell length a length_a	60.160 Å
Unit-cell length b length_b	175.870 Å
Unit-cell length c length_c	71.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	43.637 Å
R factor r_factor	0.1895
R_work r_work	0.1871
R_free r_free	0.2262

fit	/app/data/saxs_computation/u1/4u1f/4u1f.fit
pddf	/app/data/pr_computation/u1/4u1f/4u1f.pr.out
profile	/app/data/saxs_computation/u1/4u1f/4u1f.dat

Crystal structure of middle domain of eukaryotic translation initiation factor eIF3b

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

Eukaryotic translation initiation factor 3 subunit B

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)