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3fht

Crystal structure of human Dbp5 in complex with AMPPNP and RNA

Method: X-RAY DIFFRACTION Dmax: 117.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP-dependent RNA helicase DDX19B

Homo sapiens

UniProt Q9UMR2

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 68–479 Fragment：Helicase ATP-binding domain, C-terminal domain, residues 68-479 ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') ; × 1 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
2 Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts Chain B； UniProt 68–479 Fragment：Helicase ATP-binding domain, C-terminal domain, residues 68-479 ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') ; × 1 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

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 3FHT 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
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
3G0H Human dead-box RNA helicase DDX19, in complex with an ATP-analogue and RNA Deposited 2009-01-28 Different construct 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 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 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 1–412； UniProt 68–479 Author chain B； PDBConstruct 1–412； UniProt 68–479

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3fht

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3fht
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fht
Deposition date deposition_date2008-12-10
Structure title titleCrystal structure of human Dbp5 in complex with AMPPNP and RNA
Keywords keywords;Dbp5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, Nup214, CAN, Nup159, DDX19b, nuclear pore, gle1, ATP-binding, Helicase, Hydrolase, Membrane, mRNA transport, Nuclear pore complex, Nucleotide-binding, Nucleus, Phosphoprotein, Protein transport, RNA-binding, Translocation, Transport, HYDROLASE-RNA COMPLEX ;; HYDROLASE/RNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.62 Å
Radius of gyration Rg (electron density) rg_electron35.29 Å
Forward intensity I(0) i0141032000.00
Molecular weight molecular_weight93130.0 kDa
Excluded volume excluded_volume115710 ų
Envelope volume envelope_volume149000 ų
Hydration-shell volume shell_volume36077 ų
Envelope diameter envelope_diameter123.6 Å
Shell Rg shell_rg40.41 Å
Envelope Rg envelope_rg34.97 Å
Shape Rg shape_rg35.28 Å
Total Rg total_rg35.70 Å
Total atoms total_atoms6503
Residues n_residues791
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax117.7 Å
Rg (real space) rg_real35.87 Å
Rg uncertainty (real space) rg_real_error0.83 Å
I(0) (real space) i0_real1.4100e+08
I(0) uncertainty (real space) i0_real_error2.0000e+06
Rg (reciprocal space) rg_reciprocal35.72 Å
I(0) (reciprocal space) i0_reciprocal141000000.0000
Solution quality estimate total_estimate0.8146
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.4 Å
Skewness Skewness skewness0.411
Kurtosis Kurtosis kurtosis-0.653
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51720000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.704; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.713; Smooth: 0.760
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3fhta1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.0 — automated matches
Domain ID domain_idd3fhta2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.0 — automated matches
Domain ID domain_idd3fhtb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.0 — automated matches
Domain ID domain_idd3fhtb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id3fhtA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3fhtA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3fhtB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3fhtB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)