SAXSdb — 5dqs

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

Elongation factor 1-gamma

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–218	Fragment：UNP RESIDUES 2-218 Non-standard monomer：Yes (specific site not provided by mmCIF)	Elongation factor 1-beta × 1 （P24534）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；glycerol ethoxylate	Resolution 2.10 Å R-free 0.242

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 5DQS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PBU Solution structure of the C-terminal domain of the human eEF1Bgamma subunit Deposited 2003-05-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 276–437（162 aa） Fragment：C-terminal domain (residues 276-437)	Mutation：V289A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 75mM KCl；Pressure ambient NMR sample composition 1mM eEF1Bgamma[276-437]U-15N,13C, 20mM Tris-HCl pH7.5, 75mM KCl, 1mM DTT, 0.02%NaN3 (w/v) \| 95% H2O/5% D2O NMR sample composition 1mM eEF1Bgamma[276-437]U-15N, 20mM Tris-HCl pH7.5, 75mM KCl, 1mM DTT, 0.02%NaN3 (w/v) \| 95% H2O/5% D2O	Resolution not provided
5JPO Complex structure of human elongation factor 1B gamma GST-liked domain and delta N-terminal domain Deposited 2016-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–218（218 aa） Fragment：UNP RESIDUES 1-218 Chain B 1–218（218 aa） Fragment：UNP RESIDUES 1-218 Chain C 1–218（218 aa） Fragment：UNP RESIDUES 1-218 Chain D 1–218（218 aa） Fragment：UNP RESIDUES 1-218	Not recorded	GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；SOKALAN CP7, KCl, HEPES	Resolution 2.00 Å R-free 0.203

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EF1G_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–220； UniProt 2–218

Elongation factor 1-beta

Homo sapiens

UniProt P24534

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–88	Fragment：UNP RESIDUES 1-88	Elongation factor 1-gamma × 1 （P26641）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；glycerol ethoxylate	Resolution 2.10 Å R-free 0.242

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 5DQS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B64 SOLUTION STRUCTURE OF THE GUANINE NUCLEOTIDE EXCHANGE FACTOR DOMAIN FROM HUMAN ELONGATION FACTOR-ONE BETA, NMR, 20 STRUCTURES Deposited 1999-01-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 135–224（90 aa） Fragment：GUANINE EXCHANGE FACTOR DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；303 K；Ionic strength (raw mmCIF value) 100 mM；Pressure 1 NMR sample composition 95% H2O AND 5% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EF1B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 3–90； UniProt 1–88

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	5dqs
Deposition date deposition_date	2015-09-15
Structure title title	Complex structure of human elongation factor 1B alpha and gamma GST-like domains
Keywords keywords	eEF1B, elongation factor, 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	21.85 Å
Radius of gyration Rg (electron density) rg_electron	20.87 Å
Forward intensity I(0) i0	17665700.00
Molecular weight molecular_weight	32288.0 kDa
Excluded volume excluded_volume	40516 Å³
Envelope volume envelope_volume	47272 Å³
Hydration-shell volume shell_volume	19754 Å³
Envelope diameter envelope_diameter	77.3 Å
Shell Rg shell_rg	26.79 Å
Envelope Rg envelope_rg	21.26 Å
Shape Rg shape_rg	20.85 Å
Total Rg total_rg	21.75 Å
Total atoms total_atoms	2273
Residues n_residues	294
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	75.7 Å
Rg (real space) rg_real	21.87 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.7670e+07
I(0) uncertainty (real space) i0_real_error	2.1960e+05
Rg (reciprocal space) rg_reciprocal	21.87 Å
I(0) (reciprocal space) i0_reciprocal	17670000.0000
Solution quality estimate total_estimate	0.8684
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.383
Kurtosis Kurtosis kurtosis	-0.221
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3075000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.963

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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	Elongation factor 1-gamma
Molecular weight formula_weight	24865.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2330

GAMAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVFESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILGLLDAYLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLCEKMAQFDA

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 polymer

Description description	Elongation factor 1-beta
Molecular weight formula_weight	9669.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GAMGFGDLKSPAGLQVLNDYLADKSYIEGYVPSQADVAVFEAVSSPPPADLCHALRWYNHIKSYEKEKASLPGVKKALGKYGPADVEDTT

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5dqsA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5dqsA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	50.788 Å
Unit-cell length b length_b	50.788 Å
Unit-cell length c length_c	187.439 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	43.984 Å
R factor r_factor	0.2079
R_work r_work	0.2040
R_free r_free	0.2416

fit	/app/data/saxs_computation/dq/5dqs/5dqs.fit
pddf	/app/data/pr_computation/dq/5dqs/5dqs.pr.out
profile	/app/data/saxs_computation/dq/5dqs/5dqs.dat

Complex structure of human elongation factor 1B alpha and gamma GST-like domains

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

Elongation factor 1-gamma

State in the Current Structure

Other States of the Same Protein in the Database

Elongation factor 1-beta

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 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)