SAXSdb — 4ncf

▼

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

Eukaryotic translation initiation factor 5B

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 399–852	Fragment：unp residues 399-852	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；283 K；8 % PEG 8000 0.37 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 3.02 Å R-free 0.281
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 399–852	Fragment：unp residues 399-852	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；283 K；8 % PEG 8000 0.37 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 3.02 Å R-free 0.281

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 4NCF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WBI Crystal structure analysis of eukaryotic translation initiation factor 5B structure I Deposited 2013-05-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 401–1002（602 aa） Fragment：UNP residues 401-1002	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.2M Tri-Sodium Citrate, 19% PEG 3350, HEPES pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.268
3WBJ Crystal structure analysis of eukaryotic translation initiation factor 5B structure II Deposited 2013-05-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 401–855（455 aa） Fragment：UNP residues 401-855	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.1M Tris-HCl pH 8.0, 40% PEG 400, 0.2M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.256
3WBK crystal structure analysis of eukaryotic translation initiation factor 5B and 1A complex Deposited 2013-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 401–1002（602 aa） Fragment：UNP residues 401-1002	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；100mM Tris-HCl pH 8.2, 12.5%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.317
3WBK crystal structure analysis of eukaryotic translation initiation factor 5B and 1A complex Deposited 2013-05-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 401–1002（602 aa） Fragment：UNP residues 401-1002	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；100mM Tris-HCl pH 8.2, 12.5%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.317
4N3S Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae, apo form Deposited 2013-10-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 399–852（454 aa） Fragment：unp residues 399-852	Not recorded	GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；5 % PEG 3350 and 20 mM MgCl2., VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.83 Å R-free 0.194
4N3S Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae, apo form Deposited 2013-10-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 399–852（454 aa） Fragment：unp residues 399-852	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；5 % PEG 3350 and 20 mM MgCl2., VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.83 Å R-free 0.194
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric	Chain CP 401–739（339 aa） Fragment：DOMAIN 1 AND 2, RESIDUES 401-739	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,	Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric	Chain CV 401–739（339 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,	Resolution 6.60 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric	Chain 1 401–1000（600 aa）	Not recorded	ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IF2P_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–457； UniProt 399–852 Author chain B； PDBConstruct 4–457； UniProt 399–852

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ncf
Deposition date deposition_date	2013-10-24
Structure title title	Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae in complex with GDP
Keywords keywords	Translation initiation, GTPase, eIF5B/IF2, Subunit joining, Ribosome, TRANSLATION; TRANSLATION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	31.53 Å
Radius of gyration Rg (electron density) rg_electron	30.64 Å
Forward intensity I(0) i0	142653000.00
Molecular weight molecular_weight	95469.0 kDa
Excluded volume excluded_volume	120020 Å³
Envelope volume envelope_volume	155780 Å³
Hydration-shell volume shell_volume	42209 Å³
Envelope diameter envelope_diameter	103.5 Å
Shell Rg shell_rg	37.93 Å
Envelope Rg envelope_rg	30.13 Å
Shape Rg shape_rg	30.68 Å
Total Rg total_rg	31.21 Å
Total atoms total_atoms	6699
Residues n_residues	877
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	98.2 Å
Rg (real space) rg_real	31.79 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	1.3970e+08
I(0) uncertainty (real space) i0_real_error	1.6760e+06
Rg (reciprocal space) rg_reciprocal	31.44 Å
I(0) (reciprocal space) i0_reciprocal	142700000.0000
Solution quality estimate total_estimate	0.7128
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.2 Å
Skewness Skewness skewness	0.234
Kurtosis Kurtosis kurtosis	-0.328
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	4.0730
Highest regularization parameter α highest_alpha	44040000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 0.927; Sysdev: 0.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.707

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Eukaryotic translation initiation factor 5B
Molecular weight formula_weight	50998.6 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	6699

SHMNKKDLRSPICCILGHVDTGKTKLLDKIRQTNVQGGEAGGITQQIGATYFPIDAIKAKTKVMAEYEKQTFDVPGLLVIDTPGHESFSNLRSRGSSLCNIAILVIDIMHGLEQQTIESIKLLRDRKAPFVVALNKIDRLYDWKAIPNNSFRDSFAKQSRAVQEEFQSRYSKIQLELAEQGLNSELYFQNKNMSKYVSIVPTSAVTGEGVPDLLWLLLELTQKRMSKQLMYLSHVEATILEVKVVEGFGTTIDVILSNGYLREGDRIVLCGMNGPIVTNIRALLTPQPLRELRLKSEYVHHKEVKAALGVKIAANDLEKAVSGSRLLVVGPEDDEDELMDDVMDDLTGLLDSVDTTGKGVVVQASTLGSLEALLDFLKDMKIPVMSIGLGPVYKRDVMKASTMLEKAPEYAVMLCFDVKVDKEAEQYAEQEGIKIFNADVIYHLFDSFTAYQEKLLE

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 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

▼

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4ncfA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4ncfA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	4ncfA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10050 — Translation initiation factor IF- 2, domain 3

Domain ID domain_id	4ncfB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4ncfB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	4ncfB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10050 — Translation initiation factor IF- 2, domain 3

▶

8. Citations (1)

▶

Unit-cell length a length_a	73.560 Å
Unit-cell length b length_b	119.460 Å
Unit-cell length c length_c	120.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.015 Å
Low-resolution limit resolution_low	46.664 Å
R factor r_factor	0.2540
R_work r_work	0.2525
R_free r_free	0.2808

fit	/app/data/saxs_computation/nc/4ncf/4ncf.fit
pddf	/app/data/pr_computation/nc/4ncf/4ncf.pr.out
profile	/app/data/saxs_computation/nc/4ncf/4ncf.dat

Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae in complex with GDP

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

Eukaryotic translation initiation factor 5B

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