SAXSdb — 4iul

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

Eukaryotic translation initiation factor 4 gamma 2

Homo sapiens

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 61–323	Fragment：MIF4G domain, UNP residues 61-323	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M HEPES pH 7.5, 0.2 M ammonium sulfate and 18 20% (w/v) polyethylene glycol 5000 monomethyl ether, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.256
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 61–323	Fragment：MIF4G domain, UNP residues 61-323	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M HEPES pH 7.5, 0.2 M ammonium sulfate and 18 20% (w/v) polyethylene glycol 5000 monomethyl ether, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.256
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 61–323 Chain B； UniProt 61–323	Fragment：MIF4G domain, UNP residues 61-323	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M HEPES pH 7.5, 0.2 M ammonium sulfate and 18 20% (w/v) polyethylene glycol 5000 monomethyl ether, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.256

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 4IUL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3D3M The Crystal Structure of the C-terminal region of Death Associated Protein 5(DAP5) Deposited 2008-05-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 730–897（168 aa） Fragment：C terminal Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions Microbatch under oil；pH 6；293 K；100mM MMT (D,L Maleic acid, MES and Tris) pH=6, and 20% PEG 1,500, Microbatch under oil, temperature 293K	Resolution 1.90 Å R-free 0.259
3D3M The Crystal Structure of the C-terminal region of Death Associated Protein 5(DAP5) Deposited 2008-05-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 730–897（168 aa） Fragment：C terminal Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions Microbatch under oil；pH 6；293 K；100mM MMT (D,L Maleic acid, MES and Tris) pH=6, and 20% PEG 1,500, Microbatch under oil, temperature 293K	Resolution 1.90 Å R-free 0.259
3L6A Crystal structure of the C-terminal region of Human p97 Deposited 2009-12-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 540–897（358 aa） Fragment：C-terminal region, UNP residues 540-897	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；2.1M (NH4)2SO4, 0.1M MES pH 6.0, 2% PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.00 Å R-free 0.250
9JJ7 The crystal structure of SARS-CoV-2 NSP5 in complex with eIF4G2 Deposited 2024-09-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 446–455（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M MES pH 5.6, 7% PEG 6000, and 6% dimethyl sulfoxide (DMSO)	Resolution 1.80 Å R-free 0.212

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IF4G2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–268； UniProt 61–323 Author chain B； PDBConstruct 6–268； UniProt 61–323

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	4iul
Deposition date deposition_date	2013-01-21
Structure title title	MIF4G domain of DAP5
Keywords keywords	HEAT repeats, protein-protein interaction, eIF4A, 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	27.94 Å
Radius of gyration Rg (electron density) rg_electron	27.18 Å
Forward intensity I(0) i0	49036400.00
Molecular weight molecular_weight	54843.0 kDa
Excluded volume excluded_volume	69054 Å³
Envelope volume envelope_volume	88998 Å³
Hydration-shell volume shell_volume	27753 Å³
Envelope diameter envelope_diameter	96.7 Å
Shell Rg shell_rg	33.81 Å
Envelope Rg envelope_rg	27.34 Å
Shape Rg shape_rg	27.16 Å
Total Rg total_rg	27.94 Å
Total atoms total_atoms	3835
Residues n_residues	469
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	93.6 Å
Rg (real space) rg_real	27.96 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	4.9040e+07
I(0) uncertainty (real space) i0_real_error	7.0020e+05
Rg (reciprocal space) rg_reciprocal	27.96 Å
I(0) (reciprocal space) i0_reciprocal	49040000.0000
Solution quality estimate total_estimate	0.8920
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.2 Å
Skewness Skewness skewness	0.327
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9307000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.962

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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 4 gamma 2
Molecular weight formula_weight	30740.9 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	4059

GAMGSNSAANNSANEKERHDAIFRKVRGILNKLTPEKFDKLCLELLNVGVESKLILKGVILLIVDKALEEPKYSSLYAQLCLRLAEDAPNFDGPAAEGQPGQKQSTTFRRLLISKLQDEFENRTRNVDVYDKRENPLLPEEEEQRAIAKIKMLGNIKFIGELGKLDLIHESILHKCIKTLLEKKKRVQLKDMGEDLECLCQIMRTVGPRLDHERAKSLMDQYFARMCSLMLSKELPARIRFLLQDTVELREHHWVPRKAFLDNGPKTI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4iulA00
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	4iulB00
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	167.696 Å
Unit-cell length b length_b	56.696 Å
Unit-cell length c length_c	74.374 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2240
R_work r_work	0.2210
R_free r_free	0.2560

fit	/app/data/saxs_computation/iu/4iul/4iul.fit
pddf	/app/data/pr_computation/iu/4iul/4iul.pr.out
profile	/app/data/saxs_computation/iu/4iul/4iul.dat

MIF4G domain of DAP5

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

Eukaryotic translation initiation factor 4 gamma 2

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