SAXSdb — 3g0h

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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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 54–475	Fragment：UNP residues 54-275	5'-R(PUPUPUPUPUPUPU)-3' × 1 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

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 3G0H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3EWS Human DEAD-box RNA-helicase DDX19 in complex with ADP Deposited 2008-10-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–475（422 aa） Fragment：Helicase ATP-binding domain, Helicase C-terminal domain, UNP residues 54-475	Not recorded	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
3EWS Human DEAD-box RNA-helicase DDX19 in complex with ADP Deposited 2008-10-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 54–475（422 aa） Fragment：Helicase ATP-binding domain, Helicase C-terminal domain, UNP residues 54-475	Not recorded	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
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 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 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 ligand/ion 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 ligand/ion 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
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 oligomeric state 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 oligomeric state 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 14 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 3–424； 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	3g0h
Deposition date deposition_date	2009-01-28
Structure title title	Human dead-box RNA helicase DDX19, in complex with an ATP-analogue and RNA
Keywords keywords	;PROTEIN-RNA COMPLEX, DBP5, Structural Genomics, Structural Genomics Consortium, SGC, ATP-binding, Helicase, Hydrolase, Membrane, mRNA transport, Nuclear pore complex, Nucleotide-binding, Nucleus, Phosphoprotein, Protein transport, RNA-binding, Translocation, Transport, polyURACIL, HYDROLASE-RNA COMPLEX ;; HYDROLASE/RNA
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	22.18 Å
Radius of gyration Rg (electron density) rg_electron	21.30 Å
Forward intensity I(0) i0	41720700.00
Molecular weight molecular_weight	48537.0 kDa
Excluded volume excluded_volume	60187 Å³
Envelope volume envelope_volume	70195 Å³
Hydration-shell volume shell_volume	26617 Å³
Envelope diameter envelope_diameter	69.9 Å
Shell Rg shell_rg	28.72 Å
Envelope Rg envelope_rg	21.54 Å
Shape Rg shape_rg	21.31 Å
Total Rg total_rg	22.11 Å
Total atoms total_atoms	3388
Residues n_residues	415
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	67.8 Å
Rg (real space) rg_real	22.04 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	4.1720e+07
I(0) uncertainty (real space) i0_real_error	4.9400e+05
Rg (reciprocal space) rg_reciprocal	22.07 Å
I(0) (reciprocal space) i0_reciprocal	41720000.0000
Solution quality estimate total_estimate	0.9039
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.208
Kurtosis Kurtosis kurtosis	-0.403
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11950000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ATP-dependent RNA helicase DDX19B
Molecular weight formula_weight	48025.2 kDa
EC 编号 ec_number	3.6.1.-
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	3388

SMEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLDEIE

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	5'-R(PUPUPUPUPUPUP*U)-3'
Molecular weight formula_weight	2098.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

UUUUUUU

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3g0ha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d3g0ha2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	3g0hA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2170 —

Domain ID domain_id	3g0hA02
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	3g0hA03
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	41.570 Å
Unit-cell length b length_b	81.080 Å
Unit-cell length c length_c	124.740 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	29.620 Å
R factor r_factor	0.2201
R_work r_work	0.2172
R_free r_free	0.2752

fit	/app/data/saxs_computation/g0/3g0h/3g0h.fit
pddf	/app/data/pr_computation/g0/3g0h/3g0h.pr.out
profile	/app/data/saxs_computation/g0/3g0h/3g0h.dat

Human dead-box RNA helicase DDX19, in complex with an ATP-analogue and RNA

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)