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3pbp

Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex

Method: X-RAY DIFFRACTION Dmax: 188.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin NUP82

Saccharomyces cerevisiae

UniProt P40368

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 1–452 Fragment：N-terminal domain (NTD), UNP residues 1-452 Mutation：C396S Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP116/NSP116 × 1 （Q02630） Nucleoporin NUP159 × 1 （P40477） 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 1–452 Fragment：N-terminal domain (NTD), UNP residues 1-452 Mutation：C396S Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP116/NSP116 × 1 （Q02630） Nucleoporin NUP159 × 1 （P40477） 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
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain G； UniProt 1–452 Fragment：N-terminal domain (NTD), UNP residues 1-452 Mutation：C396S Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP116/NSP116 × 1 （Q02630） Nucleoporin NUP159 × 1 （P40477） 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
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain J； UniProt 1–452 Fragment：N-terminal domain (NTD), UNP residues 1-452 Mutation：C396S Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP116/NSP116 × 1 （Q02630） Nucleoporin NUP159 × 1 （P40477） 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

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 3PBP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3TKN Structure of the Nup82-Nup159-Nup98 heterotrimer Deposited 2011-08-28 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–452（452 aa） Fragment：UNP residues 1-452
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 mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–452（452 aa） Fragment：UNP residues 1-452
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 mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–452（452 aa） Fragment：UNP residues 1-452
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
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain u 1–713（713 aa）
Chain v 1–713（713 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain u 1–713（713 aa）
Chain v 1–713（713 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain u 1–713（713 aa）
Chain v 1–713（713 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

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

View Construct and Data Evidence
UniProt name NUP82_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–452； UniProt 1–452 Author chain D； PDBConstruct 1–452； UniProt 1–452 Author chain G； PDBConstruct 1–452； UniProt 1–452 Author chain J； PDBConstruct 1–452； UniProt 1–452

Nucleoporin NUP116/NSP116

Saccharomyces cerevisiae

UniProt Q02630

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 967–1113 Fragment：C-terminal domain (CTD), UNP residues 967-1113 Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP159 × 1 （P40477） 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain E； UniProt 967–1113 Fragment：C-terminal domain (CTD), UNP residues 967-1113 Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP159 × 1 （P40477） 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
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain H； UniProt 967–1113 Fragment：C-terminal domain (CTD), UNP residues 967-1113 Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP159 × 1 （P40477） 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
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain K； UniProt 967–1113 Fragment：C-terminal domain (CTD), UNP residues 967-1113 Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP159 × 1 （P40477） 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

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 3PBP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2AIV Multiple conformations in the ligand-binding site of the yeast nuclear pore targeting domain of NUP116P Deposited 2005-08-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 967–1113（147 aa） Fragment：C-terminal domain, residues 967-1113
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 100mM sodium-potassium phosphate pH 6.5, 50mM NaCl, 1mM DTT；Pressure 1
NMR sample composition 0.5-1mM Nup116p U-15N,13C | 100mM sodium-potassium phosphate pH 6.5, 50mM NaCl, 1mM DTT, 90% H2O, 10% D2O
Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NU116_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–148； UniProt 967–1113 Author chain E； PDBConstruct 2–148； UniProt 967–1113 Author chain H； PDBConstruct 2–148； UniProt 967–1113 Author chain K； PDBConstruct 2–148； UniProt 967–1113

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 1425–1460 Fragment：Tail, UNP residues 1425-1460 Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP116/NSP116 × 1 （Q02630） 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain F； UniProt 1425–1460 Fragment：Tail, UNP residues 1425-1460 Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP116/NSP116 × 1 （Q02630） 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
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain I； UniProt 1425–1460 Fragment：Tail, UNP residues 1425-1460 Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP116/NSP116 × 1 （Q02630） 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
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain L； UniProt 1425–1460 Fragment：Tail, UNP residues 1425-1460 Non-standard monomer：Yes (specific site not provided by mmCIF) Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP116/NSP116 × 1 （Q02630） 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

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 3PBP 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 oligomeric state 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
3RRM S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp 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 × 3 PDB declaration: trimeric
Chain C 2–387（386 aa） Fragment：unp residues 2-387
Not recorded 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
3TKN Structure of the Nup82-Nup159-Nup98 heterotrimer Deposited 2011-08-28 Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 9 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 1–36； UniProt 1425–1460 Author chain F； PDBConstruct 1–36； UniProt 1425–1460 Author chain I； PDBConstruct 1–36； UniProt 1425–1460 Author chain L； PDBConstruct 1–36； UniProt 1425–1460

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 3pbp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3pbp
Deposition date deposition_date2010-10-20
Structure title titleStructure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex
Keywords keywords;beta-propeller, nucleoporin, mRNA export, mRNP remodelling, NUCLEOCYTOPLASMIC Transport, PROTEIN TRANSPORT, TRANSLOCATION, TRANSPORT, autoproteolysis, Fusion protein, PROTOONCOGENE, ONCOPROTEIN, Protein COMPLEX, Nucleus, Nuclear Envelope, Nuclear Pore Complex, TRANSPORT PROTEIN, STRUCTURAL PROTEIN ;; TRANSPORT PROTEIN,STRUCTURAL PROTEIN
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_guinier57.20 Å
Radius of gyration Rg (electron density) rg_electron57.18 Å
Forward intensity I(0) i01071150000.00
Molecular weight molecular_weight280440.0 kDa
Excluded volume excluded_volume353060 ų
Envelope volume envelope_volume532390 ų
Hydration-shell volume shell_volume80302 ų
Envelope diameter envelope_diameter196.9 Å
Shell Rg shell_rg56.23 Å
Envelope Rg envelope_rg55.39 Å
Shape Rg shape_rg57.21 Å
Total Rg total_rg57.05 Å
Total atoms total_atoms19653
Residues n_residues2401
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 dmax188.9 Å
Rg (real space) rg_real57.22 Å
Rg uncertainty (real space) rg_real_error1.83 Å
I(0) (real space) i0_real1.0710e+09
I(0) uncertainty (real space) i0_real_error2.1000e+07
Rg (reciprocal space) rg_reciprocal57.15 Å
I(0) (reciprocal space) i0_reciprocal1071000000.0000
Solution quality estimate total_estimate0.8766
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary77.0 Å
Skewness Skewness skewness0.223
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha62110000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.667
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3pbpB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily10 — Peptidase S59, nucleoporin
Domain ID domain_id3pbpE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily10 — Peptidase S59, nucleoporin
Domain ID domain_id3pbpH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily10 — Peptidase S59, nucleoporin
Domain ID domain_id3pbpK00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily10 — Peptidase S59, nucleoporin
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8. Citations (1)

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9. Files and Curves (10)