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3rrm

S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp

Method: X-RAY DIFFRACTION Dmax: 124.0 Å Quality: GOOD
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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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 91–482 Fragment：unp residues 91-482 Mutation：L327V Nucleoporin GLE1 × 1 （Q12315） Nucleoporin NUP159 × 1 （P40477） 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

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 3RRM 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
3PEU S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6 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 heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 297–482（186 aa） Fragment：Dbp5-CTD
Mutation：L327V,H337R 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 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
3PEU S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6 Deposited 2010-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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,H337R 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 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
3PEV S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 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 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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
3RRN S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6 Deposited 2011-04-29 Different oligomeric state 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 10 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 4–395； UniProt 91–482

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 244–538 Fragment：unp residues 244-538 Mutation：H337R ATP-dependent RNA helicase DBP5 × 1 （P20449） Nucleoporin NUP159 × 1 （P40477） 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

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 3RRM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3PEU S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6 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 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 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
3PEU S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6 Deposited 2010-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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
3PEV S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 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 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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
3RRN S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6 Deposited 2011-04-29 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 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 oligomeric state 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 oligomeric state 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 7 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

Nucleoporin NUP159

Saccharomyces cerevisiae

UniProt P40477

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 C； UniProt 2–387 Fragment：unp residues 2-387 ATP-dependent RNA helicase DBP5 × 1 （P20449） Nucleoporin GLE1 × 1 （Q12315） 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

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 3RRM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1XIP Crystal Structure of the N-terminal Domain of Nup159 Deposited 2004-09-21 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 2–387（386 aa） Fragment：N-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 4.6；292 K；PEG3350, ammonium acetate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.50 Å R-free 0.249
3PBP Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex Deposited 2010-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1425–1460（36 aa） Fragment：Tail, UNP residues 1425-1460
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, SITTING DROP；pH 6.6；298 K；PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.60 Å R-free 0.272
3PBP Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex Deposited 2010-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1425–1460（36 aa） Fragment：Tail, UNP residues 1425-1460
Non-standard monomer：Yes (specific site not provided by mmCIF) PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；298 K；PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.60 Å R-free 0.272
3PBP Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex Deposited 2010-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1425–1460（36 aa） Fragment：Tail, UNP residues 1425-1460
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, SITTING DROP；pH 6.6；298 K；PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.60 Å R-free 0.272
3PBP Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex Deposited 2010-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1425–1460（36 aa） Fragment：Tail, UNP residues 1425-1460
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, SITTING DROP；pH 6.6；298 K；PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.60 Å R-free 0.272
3TKN Structure of the Nup82-Nup159-Nup98 heterotrimer Deposited 2011-08-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1425–1460（36 aa） Fragment：UNP residues 1425-1460
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；18.5% PEG3350, 100 mM potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.40 Å R-free 0.285
3TKN Structure of the Nup82-Nup159-Nup98 heterotrimer Deposited 2011-08-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1425–1460（36 aa） Fragment：UNP residues 1425-1460
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；18.5% PEG3350, 100 mM potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.40 Å R-free 0.285
3TKN Structure of the Nup82-Nup159-Nup98 heterotrimer Deposited 2011-08-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1425–1460（36 aa） Fragment：UNP residues 1425-1460
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；18.5% PEG3350, 100 mM potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.40 Å R-free 0.285
4DS1 The Structure of a Yeast Dyn2-Nup159 Complex and the Molecular Basis for the Dynein Light Chain - Nuclear Pore Interaction Deposited 2012-02-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1116–1126（11 aa） Fragment：UNP residues 1116-1126
Chain D 1116–1126（11 aa） Fragment：UNP residues 1116-1126
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.3 M Ammonium acetate, 5% methyl pentanediol (v/v), 35% PEG 4000 (w/v), pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.85 Å R-free 0.187
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 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 × 448 PDB declaration: 448-meric
Chain w 1–1460（1460 aa）
Chain x 1–1460（1460 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)
Resolution 37.00 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain w 1–1460（1460 aa）
Chain x 1–1460（1460 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)
Resolution 37.00 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain w 1–1460（1460 aa）
Chain x 1–1460（1460 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)
Resolution 37.00 Å

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

View Construct and Data Evidence
UniProt name NU159_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 3–388； UniProt 2–387

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 3rrm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3rrm
Deposition date deposition_date2011-04-29
Structure title titleS. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp
Keywords keywordsRecA, DEAD-box, HEAT-repeat, beta-propeller, ATPase, Helicase, mRNA-export, Nuclear Pore, HYDROLASE; HYDROLASE
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_guinier36.83 Å
Radius of gyration Rg (electron density) rg_electron36.74 Å
Forward intensity I(0) i0207267000.00
Molecular weight molecular_weight118350.0 kDa
Excluded volume excluded_volume149030 ų
Envelope volume envelope_volume191480 ų
Hydration-shell volume shell_volume44557 ų
Envelope diameter envelope_diameter125.8 Å
Shell Rg shell_rg41.73 Å
Envelope Rg envelope_rg36.19 Å
Shape Rg shape_rg36.76 Å
Total Rg total_rg37.02 Å
Total atoms total_atoms8323
Residues n_residues1040
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 dmax124.0 Å
Rg (real space) rg_real37.03 Å
Rg uncertainty (real space) rg_real_error1.53 Å
I(0) (real space) i0_real2.0730e+08
I(0) uncertainty (real space) i0_real_error3.7060e+06
Rg (reciprocal space) rg_reciprocal36.91 Å
I(0) (reciprocal space) i0_reciprocal207200000.0000
Solution quality estimate total_estimate0.8505
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.6 Å
Skewness Skewness skewness0.445
Kurtosis Kurtosis kurtosis-0.508
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha76430000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.833; Smooth: 0.844
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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_idd3rrma1
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_idd3rrma2
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_idd3rrmc1
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.14 — Nucleoporin domain
Family Family familyb.69.14.1 — Nucleoporin domain
Domain ID domain_idd3rrmc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id3rrmA01
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_id3rrmA02
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_id3rrmB00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily510 — GLE1-like
Domain ID domain_id3rrmC00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
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8. Citations (1)

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9. Files and Curves (10)