SAXSdb — 5jpo

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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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 1–218 Chain B； UniProt 1–218 Chain C； UniProt 1–218 Chain D； UniProt 1–218	Fragment：UNP RESIDUES 1-218	Elongation factor 1-delta × 2 （P29692） 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

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 5JPO	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 ligand/ion 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
5DQS Complex structure of human elongation factor 1B alpha and gamma GST-like domains Deposited 2015-09-15	Different construct Different mutation/modification 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 2–218（217 aa） Fragment：UNP RESIDUES 2-218	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；glycerol ethoxylate	Resolution 2.10 Å R-free 0.242

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 3–220； UniProt 1–218 Author chain B； PDBConstruct 3–220； UniProt 1–218 Author chain C； PDBConstruct 3–220； UniProt 1–218 Author chain D； PDBConstruct 3–220； UniProt 1–218

Elongation factor 1-delta

Homo sapiens

UniProt P29692

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain E； UniProt 1–30	Fragment：UNP RESIDUES 1-30	Elongation factor 1-gamma × 8 （P26641） 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

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 5JPO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MVM Solution structure of eEF1Bdelta CAR domain Deposited 2014-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 153–192（40 aa） Fragment：CAR domain (UNP residues 153-192)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Pressure ambient NMR sample composition 0.2-0.8 mM [U-13C; U-15N] eEF1Bdelta, 20 mM Tris, 200 mM sodium chloride, 0.01% DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MVN Solution structure of eEF1Bdelta CAR domain in TCTP-bound state Deposited 2014-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 153–192（40 aa） Fragment：CAR domain (UNP residues 153-192)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Pressure ambient NMR sample composition 0.2-0.8 mM [U-13C; U-15N] eEF1Bdelta, 20 mM Tris, 200 mM sodium chloride, 0.01% DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N51 NMR structure of the C-terminal region of human eukaryotic elongation factor 1B Deposited 2015-07-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 153–281（129 aa） Fragment：UNP RESIDUES 153-281	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 220；Pressure ambient NMR sample composition 0.8 mM [U-13C; U-15N] entity-1, 20 mM TRIS-2, 200 mM sodium chloride-3, 0.01 % w/v DSS-4, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	EF1D_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 3–32； UniProt 1–30

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	5jpo
Deposition date deposition_date	2016-05-04
Structure title title	Complex structure of human elongation factor 1B gamma GST-liked domain and delta N-terminal domain
Keywords keywords	eEF1B, elongation factor 1B, 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	31.36 Å
Radius of gyration Rg (electron density) rg_electron	30.37 Å
Forward intensity I(0) i0	149587000.00
Molecular weight molecular_weight	100000.0 kDa
Excluded volume excluded_volume	126270 Å³
Envelope volume envelope_volume	153720 Å³
Hydration-shell volume shell_volume	41807 Å³
Envelope diameter envelope_diameter	101.2 Å
Shell Rg shell_rg	37.85 Å
Envelope Rg envelope_rg	30.00 Å
Shape Rg shape_rg	30.34 Å
Total Rg total_rg	31.13 Å
Total atoms total_atoms	7069
Residues n_residues	886
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	99.7 Å
Rg (real space) rg_real	31.31 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	1.4960e+08
I(0) uncertainty (real space) i0_real_error	2.3700e+06
Rg (reciprocal space) rg_reciprocal	31.34 Å
I(0) (reciprocal space) i0_reciprocal	149600000.0000
Solution quality estimate total_estimate	0.8945
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-0.471
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42930000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.922

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Elongation factor 1-gamma
Molecular weight formula_weight	24725.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7603

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-delta
Molecular weight formula_weight	3979.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GAMATNFLAHEKIWFDKFKYDDAERRFYEQMN

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 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	519

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5jpoA01
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	5jpoA02
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 —

Domain ID domain_id	5jpoB01
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	5jpoB02
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 —

Domain ID domain_id	5jpoC01
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	5jpoC02
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 —

Domain ID domain_id	5jpoD01
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	5jpoD02
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	115.499 Å
Unit-cell length b length_b	101.054 Å
Unit-cell length c length_c	93.732 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.998 Å
Low-resolution limit resolution_low	44.358 Å
R factor r_factor	0.1693
R_work r_work	0.1683
R_free r_free	0.2026

fit	/app/data/saxs_computation/jp/5jpo/5jpo.fit
pddf	/app/data/pr_computation/jp/5jpo/5jpo.pr.out
profile	/app/data/saxs_computation/jp/5jpo/5jpo.dat

Complex structure of human elongation factor 1B gamma GST-liked domain and delta N-terminal domain

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-delta

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)