SAXSdb — 8i9j

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

RNA-binding protein E3

Vaccinia virus WR

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 9–70 Chain C； UniProt 96–183	Not recorded	Interferon-induced, double-stranded RNA-activated protein kinase × 1 （P19525）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 6.39 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	E3_VACCW
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain B； PDBConstruct 1–62； UniProt 9–70 Author chain C； PDBConstruct 1–88； UniProt 96–183

Interferon-induced, double-stranded RNA-activated protein kinase

Homo sapiens

UniProt P19525

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–170	Not recorded	RNA-binding protein E3 × 1 （P21605） RNA-binding protein E3 × 1 （P21605）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 6.39 Å

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 8I9J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QU6 STRUCTURE OF THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF THE PROTEIN KINASE PKR REVEALS THE MOLECULAR BASIS OF ITS DSRNA-MEDIATED ACTIVATION Deposited 1999-07-08	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 1–170（170 aa） Fragment：DSRNA-BINDING N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K	Resolution not provided
2A19 PKR kinase domain- eIF2alpha- AMP-PNP complex. Deposited 2005-06-19	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 258–551（294 aa） Fragment：PKR kinase domain Chain C 258–551（294 aa） Fragment：PKR kinase domain	Mutation：DEL(338-350) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：DEL(338-350) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 4 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.286
2A1A PKR kinase domain-eIF2alpha Complex Deposited 2005-06-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 258–551（294 aa）	Mutation：residue 3-175 Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8	Resolution 2.80 Å R-free 0.268
3UIU Crystal structure of Apo-PKR kinase domain Deposited 2011-11-06	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 254–551（298 aa） Fragment：PROTEIN KINASE DOMAIN, UNP RESIDUES 254-551	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；20% PEG 3350, 0.2M NaF, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.305
3UIU Crystal structure of Apo-PKR kinase domain Deposited 2011-11-06	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 254–551（298 aa） Fragment：PROTEIN KINASE DOMAIN, UNP RESIDUES 254-551	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；20% PEG 3350, 0.2M NaF, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.305
6D3K Crystal structure of unphosphorylated human PKR kinase domain in complex with ADP Deposited 2018-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 229–551（323 aa） Fragment：kinase domain (229-551) Chain B 229–551（323 aa） Fragment：kinase domain (229-551)	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, pH 7.5, 6% v/v PEG400, 2.0 M ammonium sulfate, protein was complexed with AMP-PNP and Mg2+ prior to crystallization	Resolution 2.60 Å R-free 0.266
6D3K Crystal structure of unphosphorylated human PKR kinase domain in complex with ADP Deposited 2018-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 229–551（323 aa） Fragment：kinase domain (229-551) Chain C 229–551（323 aa） Fragment：kinase domain (229-551)	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 PO4 PHOSPHATE ION × 3 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, pH 7.5, 6% v/v PEG400, 2.0 M ammonium sulfate, protein was complexed with AMP-PNP and Mg2+ prior to crystallization	Resolution 2.60 Å R-free 0.266
6D3L Crystal structure of unphosphorylated human PKR Deposited 2018-04-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 229–551（323 aa） Fragment：kinase domain (229-551)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris, pH 5.5, 2.0 M ammonium sulfate, 1:3 molar ratio of dp8 (heparin) was added to protein prior to crystallization	Resolution 3.10 Å R-free 0.347
6D3L Crystal structure of unphosphorylated human PKR Deposited 2018-04-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 229–551（323 aa） Fragment：kinase domain (229-551)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris, pH 5.5, 2.0 M ammonium sulfate, 1:3 molar ratio of dp8 (heparin) was added to protein prior to crystallization	Resolution 3.10 Å R-free 0.347
6NPY Cryo-EM structure of NLRP3 bound to NEK7 Deposited 2019-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 260–266（7 aa）	Mutation：L54R,V58K,P59T,K87A,A99V,S100C,E103T,D104G	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7OBK Crystal structure of 14-3-3 sigma in complex with PKR phosphopeptide Deposited 2021-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 541–551（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.095 M Hepes pH7.3, 25%PEG 400, 0.19 M CaCl2 and 5 % Glycerol	Resolution 1.80 Å R-free 0.183
7OBL Crystal structure of 14-3-3 sigma in complex with PKR phosphopeptide and stabilizer Fusicoccin-A Deposited 2021-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 541–551（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FSC FUSICOCCIN × 2 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.095 M Hepes pH7.3, 25%PEG 400, 0.19 M CaCl2 and 5 % Glycerol	Resolution 1.80 Å R-free 0.239
8BI7 Binary structure of 14-3-3s and PKR phosphopeptide Deposited 2022-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 541–551（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.095 M Hepes pH 7.1, 0.19 M CaCl2, 25% PEG400, 5% glycerol	Resolution 1.40 Å R-free 0.188
8IZN Structural study of Interferon-induced, double-stranded RNA-activated protein kinase (PKR) and Non-structural protein 1 (NS1) complex Deposited 2023-04-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–170（170 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 6.67 Å
8QEL PKR kinase domain- eIF2alpha in complex with compound Deposited 2023-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 258–337（80 aa） Chain B 357–541（185 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	UH3 (3~{Z})-3-[(4-methyl-1~{H}-imidazol-5-yl)methylidene]-2-oxidanylidene-1~{H}-indole-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MOPS pH 7.5, 10% PEG 8000, 0.2 M magnesium acetate	Resolution 2.45 Å R-free 0.278

12 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	E2AK2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 6–175； UniProt 1–170

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	8i9j
Deposition date deposition_date	2023-02-07
Structure title title	The PKR and E3L complex
Keywords keywords	E3L, PKR, Vaccinia Virus, VIRAL PROTEIN-TRANSFERASE complex; VIRAL PROTEIN/TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	33.10 Å
Radius of gyration Rg (electron density) rg_electron	33.23 Å
Forward intensity I(0) i0	23234800.00
Molecular weight molecular_weight	36599.0 kDa
Excluded volume excluded_volume	45579 Å³
Envelope volume envelope_volume	66073 Å³
Hydration-shell volume shell_volume	19705 Å³
Envelope diameter envelope_diameter	108.8 Å
Shell Rg shell_rg	33.95 Å
Envelope Rg envelope_rg	31.79 Å
Shape Rg shape_rg	33.27 Å
Total Rg total_rg	33.17 Å
Total atoms total_atoms	4446
Residues n_residues	329
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	112.5 Å
Rg (real space) rg_real	33.53 Å
Rg uncertainty (real space) rg_real_error	1.39 Å
I(0) (real space) i0_real	2.3230e+07
I(0) uncertainty (real space) i0_real_error	4.2270e+05
Rg (reciprocal space) rg_reciprocal	33.35 Å
I(0) (reciprocal space) i0_reciprocal	23230000.0000
Solution quality estimate total_estimate	0.7901
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	37.5 Å
Skewness Skewness skewness	0.428
Kurtosis Kurtosis kurtosis	-0.486
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	508900.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.556; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.749; Smooth: 0.852

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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	RNA-binding protein E3
Molecular weight formula_weight	7041.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	4446

RSNAEIVCEAIKTIGIEGATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDDIPPRWFMTT

来源 Source

来源生物 organism	Vaccinia virus WR
NCBI Class编号 ncbi_taxonomy_id	10254
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Interferon-induced, double-stranded RNA-activated protein kinase
Molecular weight formula_weight	19705.4 kDa
EC 编号 ec_number	2.7.11.1,2.7.10.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GSHMEMAGDLSAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSMGNYIGLINRIAQKKRLTVNYEQCASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQILSEETGSGC

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 polymer

Description description	RNA-binding protein E3
Molecular weight formula_weight	9916.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EDHKSFDDVIPAKKIIDWKGANPVTVINEYCQITRRDWSFRIESVGPSNSPTFYACVDIDGRVFDKADGKSKRDAKNNAAKLAVDKLL

来源 Source

来源生物 organism	Vaccinia virus WR
NCBI Class编号 ncbi_taxonomy_id	10254
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	6.39 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	307424

fit	/app/data/saxs_computation/i9/8i9j/8i9j.fit
pddf	/app/data/pr_computation/i9/8i9j/8i9j.pr.out
profile	/app/data/saxs_computation/i9/8i9j/8i9j.dat

The PKR and E3L complex

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

RNA-binding protein E3

State in the Current Structure

Other States of the Same Protein in the Database

Interferon-induced, double-stranded RNA-activated protein kinase

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

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)