SAXSdb — 5h7u

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

Eukaryotic translation initiation factor 3 subunit C

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 36–163	Fragment：UNP RESIDUES 36-163	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 170；Pressure 1 NMR sample composition：0.4 mM [U-100% 13C; U-100% 15N] eIF3c 36-163, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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 5H7U	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 p 193–206（14 aa） Chain p 251–812（562 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
4U1C Crystal structure of the eIF3a/eIF3c PCI-domain heterodimer Deposited 2014-07-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: Dimeric	Chain C 247–812（566 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 q 251–812（562 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 q 251–812（562 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 q 96–794（699 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 q 96–794（699 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 q 1–812（812 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 q 1–812（812 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
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 p 1–812（812 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
8S8K Structure of a yeast 48S-AUC preinitiation complex in swivelled conformation (model py48S-AUC-swiv-eIF1) 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 n 1–812（812 aa）	Not recorded	MG MAGNESIUM ION × 96 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 4.00 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EIF3C_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–128； UniProt 36–163

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	5h7u
Deposition date deposition_date	2016-11-21
Structure title title	NMR structure of eIF3 36-163
Keywords keywords	translation, initiation factor, eukaryotic initiation factor; TRANSLATION
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	60.77 Å
Radius of gyration Rg (electron density) rg_electron	61.89 Å
Forward intensity I(0) i0	1453580000.00
Molecular weight molecular_weight	291280.0 kDa
Excluded volume excluded_volume	352170 Å³
Envelope volume envelope_volume	782340 Å³
Hydration-shell volume shell_volume	92179 Å³
Envelope diameter envelope_diameter	357.8 Å
Shell Rg shell_rg	57.73 Å
Envelope Rg envelope_rg	89.45 Å
Shape Rg shape_rg	62.10 Å
Total Rg total_rg	61.15 Å
Total atoms total_atoms	39040
Residues n_residues	2560
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	271.1 Å
Rg (real space) rg_real	63.99 Å
Rg uncertainty (real space) rg_real_error	5.87 Å
I(0) (real space) i0_real	1.4530e+09
I(0) uncertainty (real space) i0_real_error	3.7960e+07
Rg (reciprocal space) rg_reciprocal	58.00 Å
I(0) (reciprocal space) i0_reciprocal	1439000000.0000
Solution quality estimate total_estimate	0.6151
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	10.4 Å
Skewness Skewness skewness	0.836
Kurtosis Kurtosis kurtosis	-0.083
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0017
Highest regularization parameter α highest_alpha	995300.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.000; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.993

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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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Description description	Eukaryotic translation initiation factor 3 subunit C
Molecular weight formula_weight	14598.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	39040

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/h7/5h7u/5h7u.fit
pddf	/app/data/pr_computation/h7/5h7u/5h7u.pr.out
profile	/app/data/saxs_computation/h7/5h7u/5h7u.dat

NMR structure of eIF3 36-163

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

Eukaryotic translation initiation factor 3 subunit C

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

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)