← Back to search
3peu

S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: GOOD
▼

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

ATP-dependent RNA helicase DBP5

Saccharomyces cerevisiae

UniProt P20449

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 297–482 Fragment：Dbp5-CTD Mutation：L327V,H337R Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin GLE1 × 1 （Q12315） SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；30% PEG 3350, 100 mM HEPES pH 8.0, 50 mM NaOAc, 200mM LiS04, 10 mM HEPES pH 7.5, 100mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.60 Å R-free 0.213
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 297–482 Fragment：Dbp5-CTD Mutation：L327V,H337R Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin GLE1 × 1 （Q12315） SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；30% PEG 3350, 100 mM HEPES pH 8.0, 50 mM NaOAc, 200mM LiS04, 10 mM HEPES pH 7.5, 100mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.60 Å R-free 0.213

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 3PEU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KBE solution structure of amino-terminal domain of Dbp5p Deposited 2008-11-27 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 71–296（226 aa） Fragment：amino-terminal domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 20 mM MES, 100 mM potassium acetate, 0.6 mM [U-13C; U-15N] Dbp5p, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KBF solution structure of carboxyl-terminal domain of Dbp5p Deposited 2008-11-28 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 296–482（187 aa） Fragment：residues 296-482
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 0.7 mM [U-13C; U-15N] protein, 20 mM MES, 100 mM potassium acetate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3GFP Structure of the C-terminal domain of the DEAD-box protein Dbp5 Deposited 2009-02-27 Different construct Different mutation/modification 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 296–482（187 aa） Fragment：Helicase C-terminal domain
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, HANGING DROP；pH 6.5；292 K；2M Na/K HPO4, 100mM Na cacodylate pH 6.5, 8% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.80 Å R-free 0.230
3PEV S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 Deposited 2010-10-27 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 297–482（186 aa） Fragment：Dbp5-CTD
Mutation：L327V Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；30% PEG 3350, 100 mM HEPES pH 7.8, 200mM LiS04, 10mM HEPES pH 7.5, 150mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.238
3PEV S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 Deposited 2010-10-27 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 297–482（186 aa） Fragment：Dbp5-CTD
Mutation：L327V Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；30% PEG 3350, 100 mM HEPES pH 7.8, 200mM LiS04, 10mM HEPES pH 7.5, 150mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.238
3PEW S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3 Deposited 2010-10-27 Different construct Different mutation/modification 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 91–482（392 aa）
Mutation：L327V ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 BEF BERYLLIUM TRIFLUORIDE ION × 1 NO3 NITRATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；20% PEG 3350, 200 mM MgNO3, 10 mM HEPES pH 7.5, 100 mM NaCl, 1mM DTT, 0.5 mM IP6, 5 mM MgCl2, 1 mM ADP, 3 mM BeCl2, 15 mM NaF, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.50 Å R-free 0.189
3PEY S. cerevisiae Dbp5 bound to RNA and ADP BeF3 Deposited 2010-10-27 Different construct Different mutation/modification 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 91–482（392 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 BEF BERYLLIUM TRIFLUORIDE ION × 1 NO3 NITRATE ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；20% PEG 3350, 200 mM MgNO3, 10 mM HEPES pH 7.5, 100 mM NaCl, 1mM DTT, 0.5 mM IP6, 5 mM MgCl2, 1 mM ADP, 3 mM BeCl2, 15 mM NaF, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.40 Å R-free 0.179
3RRM S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp Deposited 2011-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 91–482（392 aa） Fragment：unp residues 91-482
Mutation：L327V ADP ADENOSINE-5'-DIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；20% PEG 3350, 200 mM KOAc, 20 mM sarcosine, 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 0.5 mM IP6, 10 mM MgCl2, 1 mM ADP, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.261
3RRN S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6 Deposited 2011-04-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 91–482（392 aa） Fragment：unp residues 91-482
Mutation：L327V ADP ADENOSINE-5'-DIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；30% PEG 300, 100mM MES, 2% MPD, 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 0.5 mM IP6, 0.5 mM ADP, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5
Resolution 4.00 Å R-free 0.239

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DBP5_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–188； UniProt 297–482

Nucleoporin GLE1

Saccharomyces cerevisiae

UniProt Q12315

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 244–538 Non-standard monomer：Yes (specific site not provided by mmCIF) ATP-dependent RNA helicase DBP5 × 1 （P20449） SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；30% PEG 3350, 100 mM HEPES pH 8.0, 50 mM NaOAc, 200mM LiS04, 10 mM HEPES pH 7.5, 100mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.60 Å R-free 0.213
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 244–538 Non-standard monomer：Yes (specific site not provided by mmCIF) ATP-dependent RNA helicase DBP5 × 1 （P20449） SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；30% PEG 3350, 100 mM HEPES pH 8.0, 50 mM NaOAc, 200mM LiS04, 10 mM HEPES pH 7.5, 100mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.60 Å R-free 0.213

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 3PEU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3PEV S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 Deposited 2010-10-27 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 244–538（295 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；30% PEG 3350, 100 mM HEPES pH 7.8, 200mM LiS04, 10mM HEPES pH 7.5, 150mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.238
3PEV S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 Deposited 2010-10-27 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 244–538（295 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；30% PEG 3350, 100 mM HEPES pH 7.8, 200mM LiS04, 10mM HEPES pH 7.5, 150mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.238
3RRM S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp Deposited 2011-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 244–538（295 aa） Fragment：unp residues 244-538
Mutation：H337R ADP ADENOSINE-5'-DIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；20% PEG 3350, 200 mM KOAc, 20 mM sarcosine, 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 0.5 mM IP6, 10 mM MgCl2, 1 mM ADP, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.261
3RRN S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6 Deposited 2011-04-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 244–538（295 aa） Fragment：unp residues 244-538
Mutation：H337R ADP ADENOSINE-5'-DIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；30% PEG 300, 100mM MES, 2% MPD, 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 0.5 mM IP6, 0.5 mM ADP, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5
Resolution 4.00 Å R-free 0.239
6B4E Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex Deposited 2017-09-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 243–538（296 aa）
Not recorded PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M HEPES pH 8.2, 11 % (w/v/) PEG 3350, 0.2 M L-Proline
Resolution 1.75 Å R-free 0.211
6B4E Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex Deposited 2017-09-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 243–538（296 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M HEPES pH 8.2, 11 % (w/v/) PEG 3350, 0.2 M L-Proline
Resolution 1.75 Å R-free 0.211

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GLE1_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–297； UniProt 244–538

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 3peu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3peu
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3peu
Deposition date deposition_date2010-10-27
Structure title titleS. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6
Keywords keywordsRecA, HEAT, DEAD-box, ATPase, Helicase, mRNA export, Nuclear Pore, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier24.42 Å
Radius of gyration Rg (electron density) rg_electron23.37 Å
Forward intensity I(0) i051761300.00
Molecular weight molecular_weight55605.0 kDa
Excluded volume excluded_volume69439 ų
Envelope volume envelope_volume82063 ų
Hydration-shell volume shell_volume28858 ų
Envelope diameter envelope_diameter80.5 Å
Shell Rg shell_rg31.00 Å
Envelope Rg envelope_rg23.51 Å
Shape Rg shape_rg23.40 Å
Total Rg total_rg24.15 Å
Total atoms total_atoms3867
Residues n_residues462
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.8 Å
Rg (real space) rg_real24.30 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real5.1760e+07
I(0) uncertainty (real space) i0_real_error6.2810e+05
Rg (reciprocal space) rg_reciprocal24.33 Å
I(0) (reciprocal space) i0_reciprocal51760000.0000
Solution quality estimate total_estimate0.8956
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0 Å
Skewness Skewness skewness0.227
Kurtosis Kurtosis kurtosis-0.429
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16210000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3peua_
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 (2 domains)

Domain ID domain_id3peuA00
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_id3peuB00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily510 — GLE1-like
▶

8. Citations (1)

▶

9. Files and Curves (10)