SAXSdb — 3d3m

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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 730–897	Fragment：C terminal Domain	No other associated polymer	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 730–897	Fragment：C terminal Domain	No other associated polymer	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

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 3D3M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
4IUL MIF4G domain of DAP5 Deposited 2013-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–323（263 aa） Fragment：MIF4G domain, UNP residues 61-323	Not recorded	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
4IUL MIF4G domain of DAP5 Deposited 2013-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 61–323（263 aa） Fragment：MIF4G domain, UNP residues 61-323	Not recorded	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
4IUL MIF4G domain of DAP5 Deposited 2013-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 61–323（263 aa） Fragment：MIF4G domain, UNP residues 61-323 Chain B 61–323（263 aa） Fragment：MIF4G domain, UNP residues 61-323	Not recorded	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
9JJ7 The crystal structure of SARS-CoV-2 NSP5 in complex with eIF4G2 Deposited 2024-09-13	Different construct Different oligomeric state 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 5 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 1–168； UniProt 730–897 Author chain B； PDBConstruct 1–168； UniProt 730–897

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	3d3m
Deposition date deposition_date	2008-05-12
Structure title title	The Crystal Structure of the C-terminal region of Death Associated Protein 5(DAP5)
Keywords keywords	;HEAT repeat domain, Structural Genomics, PSI, Protein Structure Initiative, Israel Structural Proteomics Center, ISPC, Acetylation, Initiation factor, Phosphoprotein, Protein biosynthesis, Repressor, Translation regulation, 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	22.81 Å
Radius of gyration Rg (electron density) rg_electron	22.24 Å
Forward intensity I(0) i0	20564300.00
Molecular weight molecular_weight	37432.0 kDa
Excluded volume excluded_volume	48067 Å³
Envelope volume envelope_volume	55988 Å³
Hydration-shell volume shell_volume	21900 Å³
Envelope diameter envelope_diameter	81.2 Å
Shell Rg shell_rg	28.27 Å
Envelope Rg envelope_rg	22.39 Å
Shape Rg shape_rg	22.21 Å
Total Rg total_rg	23.16 Å
Total atoms total_atoms	2649
Residues n_residues	318
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	79.3 Å
Rg (real space) rg_real	22.86 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	2.0560e+07
I(0) uncertainty (real space) i0_real_error	3.2040e+05
Rg (reciprocal space) rg_reciprocal	22.85 Å
I(0) (reciprocal space) i0_reciprocal	20560000.0000
Solution quality estimate total_estimate	0.8556
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.0 Å
Skewness Skewness skewness	0.455
Kurtosis Kurtosis kurtosis	-0.227
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7613000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.726; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3d3mA00
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	3d3mB00
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	61.059 Å
Unit-cell length b length_b	45.734 Å
Unit-cell length c length_c	63.357 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.81 °
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	1.900 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2140
R_work r_work	0.2110
R_free r_free	0.2590

Description description	Eukaryotic translation initiation factor 4 gamma 2
Molecular weight formula_weight	19657.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2714

The Crystal Structure of the C-terminal region of Death Associated Protein 5(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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

fit	/app/data/saxs_computation/d3/3d3m/3d3m.fit
pddf	/app/data/pr_computation/d3/3d3m/3d3m.pr.out
profile	/app/data/saxs_computation/d3/3d3m/3d3m.dat