SAXSdb — 3ews

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

ATP-dependent RNA helicase DDX19B

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 54–475	Fragment：Helicase ATP-binding domain, Helicase C-terminal domain, UNP residues 54-475	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M ammonium acetate, 0.1M Bis-Tris, 17% PEG-10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.260
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 54–475	Fragment：Helicase ATP-binding domain, Helicase C-terminal domain, UNP residues 54-475	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M ammonium acetate, 0.1M Bis-Tris, 17% PEG-10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.260

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 3EWS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FHC Crystal structure of human Dbp5 in complex with Nup214 Deposited 2008-12-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 68–302（235 aa） Fragment：Nterminal RecA-like domain, UNP residues 68-302	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50mM MES pH 6.0, 900mM Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.260
3FHT Crystal structure of human Dbp5 in complex with AMPPNP and RNA Deposited 2008-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 68–479（412 aa） Fragment：Helicase ATP-binding domain, C-terminal domain, residues 68-479	Not recorded	MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100mM Tris pH 7.0, 20% PEG 2000 mono-methyl-ether, 3% PEG 3350, 30mM NaF, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.225
3FHT Crystal structure of human Dbp5 in complex with AMPPNP and RNA Deposited 2008-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 68–479（412 aa） Fragment：Helicase ATP-binding domain, C-terminal domain, residues 68-479	Not recorded	MG MAGNESIUM ION × 1 GOL GLYCEROL × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100mM Tris pH 7.0, 20% PEG 2000 mono-methyl-ether, 3% PEG 3350, 30mM NaF, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.225
3FMO Crystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19 Deposited 2008-12-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–300（300 aa）	Not recorded	GOL GLYCEROL × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；sodium di-hydrogen phosphate, di-potassium hydrogen phosphate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.51 Å R-free 0.242
3FMP Crystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19 Deposited 2008-12-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–479（479 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；298 K；PEG 3000, CHES buffer, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.19 Å R-free 0.283
3FMP Crystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19 Deposited 2008-12-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–479（479 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；298 K；PEG 3000, CHES buffer, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.19 Å R-free 0.283
3G0H Human dead-box RNA helicase DDX19, in complex with an ATP-analogue and RNA Deposited 2009-01-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 54–475（422 aa） Fragment：UNP residues 54-275	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；14% PEGMME 2000, 0.25M trimethylamine n-oxide, 0.1 M Tris, pH 8, VAPOR DIFFUSION, temperature 277K	Resolution 2.70 Å R-free 0.275
6B4I Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex Deposited 2017-09-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 54–479（426 aa）	Not recorded	PO4 PHOSPHATE ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；13 % (w/v) PEG 3350, 0.2 M sodium potassium phosphate	Resolution 3.62 Å R-free 0.281
6B4I Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex Deposited 2017-09-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 54–479（426 aa）	Not recorded	PO4 PHOSPHATE ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；13 % (w/v) PEG 3350, 0.2 M sodium potassium phosphate	Resolution 3.62 Å R-free 0.281
6B4J Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(AMPPNP) complex Deposited 2017-09-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 54–479（426 aa）	Not recorded	PO4 PHOSPHATE ION × 4 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；15 % (w/v) PEG 3350, 0.3 M sodium potassium phosphate pH 6.6	Resolution 3.40 Å R-free 0.313
6B4J Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(AMPPNP) complex Deposited 2017-09-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 54–479（426 aa）	Not recorded	PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；15 % (w/v) PEG 3350, 0.3 M sodium potassium phosphate pH 6.6	Resolution 3.40 Å R-free 0.313
6B4K Crystal structure of human DDX19B(AMPPNP) Deposited 2017-09-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–479（426 aa）	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MIB buffer pH 5.0 (malonate, imidazole, borate), 13 % (w/v) PEG 1500	Resolution 2.20 Å R-free 0.248
6B4K Crystal structure of human DDX19B(AMPPNP) Deposited 2017-09-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 54–479（426 aa）	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MIB buffer pH 5.0 (malonate, imidazole, borate), 13 % (w/v) PEG 1500	Resolution 2.20 Å R-free 0.248

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DD19B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–445； UniProt 54–475 Author chain B； PDBConstruct 24–445； UniProt 54–475

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	3ews
Deposition date deposition_date	2008-10-16
Structure title title	Human DEAD-box RNA-helicase DDX19 in complex with ADP
Keywords keywords	;RNA HELICASE, DEAD, ADP, Structural Genomics, Structural Genomics Consortium, SGC, rRNA, ATP-binding, Hydrolase, Nucleotide-binding, RNA-binding, mRNA, Alternative splicing, Cytoplasm, Helicase, Membrane, mRNA transport, Nuclear pore complex, Nucleus, Protein transport, Translocation, Transport ;; HYDROLASE
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	31.41 Å
Radius of gyration Rg (electron density) rg_electron	30.48 Å
Forward intensity I(0) i0	136787000.00
Molecular weight molecular_weight	92498.0 kDa
Excluded volume excluded_volume	115820 Å³
Envelope volume envelope_volume	147610 Å³
Hydration-shell volume shell_volume	39625 Å³
Envelope diameter envelope_diameter	106.6 Å
Shell Rg shell_rg	38.31 Å
Envelope Rg envelope_rg	30.25 Å
Shape Rg shape_rg	30.51 Å
Total Rg total_rg	31.06 Å
Total atoms total_atoms	6482
Residues n_residues	821
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	99.8 Å
Rg (real space) rg_real	31.32 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	1.3680e+08
I(0) uncertainty (real space) i0_real_error	2.0220e+06
Rg (reciprocal space) rg_reciprocal	31.36 Å
I(0) (reciprocal space) i0_reciprocal	136800000.0000
Solution quality estimate total_estimate	0.8896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	97.8 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.410
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	94590000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.809

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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	ATP-dependent RNA helicase DDX19B
Molecular weight formula_weight	50496.9 kDa
EC 编号 ec_number	3.6.1.-
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	6508

MHHHHHHSSGVDLGTENLYFQSMEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLDEIE

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	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3ewsA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3ewsA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3ewsB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3ewsB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	81.580 Å
Unit-cell length b length_b	47.610 Å
Unit-cell length c length_c	124.690 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.40 °
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	2.700 Å
Low-resolution limit resolution_low	19.859 Å
R factor r_factor	0.1918
R_work r_work	0.1882
R_free r_free	0.2597

fit	/app/data/saxs_computation/ew/3ews/3ews.fit
pddf	/app/data/pr_computation/ew/3ews/3ews.pr.out
profile	/app/data/saxs_computation/ew/3ews/3ews.dat

Human DEAD-box RNA-helicase DDX19 in complex with ADP

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

ATP-dependent RNA helicase DDX19B

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