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3f3f

Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21

Method: X-RAY DIFFRACTION Dmax: 224.3 Å Quality: SUSPICIOUS
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin SEH1

Saccharomyces cerevisiae

UniProt P53011

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–349 Chain B； UniProt 1–349 Chain E； UniProt 1–349 Chain F； UniProt 1–349 Not recorded Nucleoporin NUP85 × 4 （P46673） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG 10000, MES buffer, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.90 Å R-free 0.265

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 3F3F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3EWE Crystal Structure of the Nup85/Seh1 Complex Deposited 2008-10-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–349（349 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Sodium Citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.50 Å R-free 0.369
3EWE Crystal Structure of the Nup85/Seh1 Complex Deposited 2008-10-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–349（349 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Sodium Citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.50 Å R-free 0.369
3EWE Crystal Structure of the Nup85/Seh1 Complex Deposited 2008-10-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–349（349 aa）
Chain C 1–349（349 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Sodium Citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.50 Å R-free 0.369
3F3G Crystal structure of the nucleoporin pair Nup85-Seh1, space group P212121 Deposited 2008-10-30 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–349（349 aa）
Chain B 1–349（349 aa）
Chain E 1–349（349 aa）
Chain F 1–349（349 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Sodium citrate, Sodium chloride, Tris-HCl buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.75 Å R-free 0.272
3F3P Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212 Deposited 2008-10-31 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 A 1–349（349 aa）
Chain B 1–349（349 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298 K；PEG 3350, Tacsimate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.281
3F3P Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212 Deposited 2008-10-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–349（349 aa）
Chain F 1–349（349 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298 K；PEG 3350, Tacsimate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.281
3F3P Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212 Deposited 2008-10-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–349（349 aa）
Chain J 1–349（349 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298 K；PEG 3350, Tacsimate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.281
4XMM Structure of the yeast coat nucleoporin complex, space group C2 Deposited 2015-01-14 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–349（349 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 20000, ethanol, MES
Resolution 7.38 Å R-free 0.353
6X08 Nup85-Seh1 from S. cerevisiae bound by VHH-SAN2 Deposited 2020-05-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–349（349 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1M ammonium sulfate, di-sodium succinate pH 5.5, and the addition of 4% 1-propanol
Resolution 4.19 Å R-free 0.346
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 136 PDB declaration: 136-meric
Chain e 1–349（349 aa）
Chain p 1–349（349 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.60 Å
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain e 1–349（349 aa）
Chain p 1–349（349 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.60 Å
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain e 1–349（349 aa）
Chain p 1–349（349 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.60 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 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain e 1–349（349 aa）
Chain l 1–349（349 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 e 1–349（349 aa）
Chain l 1–349（349 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 e 1–349（349 aa）
Chain l 1–349（349 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
8ADL Cryo-EM structure of the SEA complex Deposited 2022-07-08 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 × 22 PDB declaration: 22-meric
Chain D 1–349（349 aa）
Chain E 1–349（349 aa）
Chain F 1–349（349 aa）
Chain L 1–349（349 aa）
Chain M 1–349（349 aa）
Chain N 1–349（349 aa）
Not recorded ZN ZINC ION × 28 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 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 × 32 PDB declaration: 32-meric
Chain D 1–349（349 aa）
Chain E 1–349（349 aa）
Chain F 1–349（349 aa）
Chain L 1–349（349 aa）
Chain M 1–349（349 aa）
Chain N 1–349（349 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

9 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SEH1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–351； UniProt 1–349 Author chain B； PDBConstruct 3–351； UniProt 1–349 Author chain E； PDBConstruct 3–351； UniProt 1–349 Author chain F； PDBConstruct 3–351； UniProt 1–349

Nucleoporin NUP85

Saccharomyces cerevisiae

UniProt P46673

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 1–570 Chain D； UniProt 1–570 Chain G； UniProt 1–570 Chain H； UniProt 1–570 Fragment：UNP residues 1-570 Nucleoporin SEH1 × 4 （P53011） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG 10000, MES buffer, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.90 Å R-free 0.265

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 3F3F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3EWE Crystal Structure of the Nup85/Seh1 Complex Deposited 2008-10-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–564（564 aa） Fragment：UNP residues 1-564
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Sodium Citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.50 Å R-free 0.369
3EWE Crystal Structure of the Nup85/Seh1 Complex Deposited 2008-10-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–564（564 aa） Fragment：UNP residues 1-564
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Sodium Citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.50 Å R-free 0.369
3EWE Crystal Structure of the Nup85/Seh1 Complex Deposited 2008-10-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–564（564 aa） Fragment：UNP residues 1-564
Chain D 1–564（564 aa） Fragment：UNP residues 1-564
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Sodium Citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.50 Å R-free 0.369
3F3G Crystal structure of the nucleoporin pair Nup85-Seh1, space group P212121 Deposited 2008-10-30 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–570（570 aa） Fragment：UNP residues 1-570
Chain D 1–570（570 aa） Fragment：UNP residues 1-570
Chain G 1–570（570 aa） Fragment：UNP residues 1-570
Chain H 1–570（570 aa） Fragment：UNP residues 1-570
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Sodium citrate, Sodium chloride, Tris-HCl buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.75 Å R-free 0.272
3F3P Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212 Deposited 2008-10-31 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 C 1–570（570 aa） Fragment：UNP residues 1-570
Chain D 1–570（570 aa） Fragment：UNP residues 1-570
Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298 K；PEG 3350, Tacsimate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.281
3F3P Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212 Deposited 2008-10-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–570（570 aa） Fragment：UNP residues 1-570
Chain H 1–570（570 aa） Fragment：UNP residues 1-570
Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298 K；PEG 3350, Tacsimate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.281
3F3P Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212 Deposited 2008-10-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain K 1–570（570 aa） Fragment：UNP residues 1-570
Chain L 1–570（570 aa） Fragment：UNP residues 1-570
Non-standard monomer：Yes (specific site not provided by mmCIF) 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；298 K；PEG 3350, Tacsimate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.281
4XMM Structure of the yeast coat nucleoporin complex, space group C2 Deposited 2015-01-14 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 44–744（701 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 20000, ethanol, MES
Resolution 7.38 Å R-free 0.353
4XMN Structure of the yeast coat nucleoporin complex, space group P212121 Deposited 2015-01-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 73–743（671 aa）
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；294 K；PEG 20000, ethanol, MES
Resolution 7.60 Å R-free 0.347
6X08 Nup85-Seh1 from S. cerevisiae bound by VHH-SAN2 Deposited 2020-05-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–564（564 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1M ammonium sulfate, di-sodium succinate pH 5.5, and the addition of 4% 1-propanol
Resolution 4.19 Å R-free 0.346
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 136 PDB declaration: 136-meric
Chain b 1–744（744 aa）
Chain m 1–744（744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.60 Å
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain b 1–744（744 aa）
Chain m 1–744（744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.60 Å
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain b 1–744（744 aa）
Chain m 1–744（744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.60 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 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain b 1–744（744 aa）
Chain i 1–744（744 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 b 1–744（744 aa）
Chain i 1–744（744 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 b 1–744（744 aa）
Chain i 1–744（744 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
8TIE Double nuclear outer ring of Nup84-complexes from the yeast NPC Deposited 2023-07-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain b 1–744（744 aa）
Chain m 1–744（744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM HEPES,50mM Potassium acetate,20mM NaCl,2mM MgCl2,1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å

9 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NUP85_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–570； UniProt 1–570 Author chain D； PDBConstruct 1–570； UniProt 1–570 Author chain G； PDBConstruct 1–570； UniProt 1–570 Author chain H； PDBConstruct 1–570； UniProt 1–570

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 3f3f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3f3f
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3f3f
Deposition date deposition_date2008-10-30
Structure title titleCrystal structure of the nucleoporin pair Nup85-Seh1, space group P21
Keywords keywords;Structural Protein, Protein Complex, Nucleoporin, Nucleoporin Complex, Nuclear Pore Complex, Macromolecular Assembly, Membrane Coat, Nucleocytoplasmic Transport, beta-propeller, solenoid domain, mRNA transport, Nucleus, Protein transport, Translocation, WD repeat ;; 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_guinier78.68 Å
Radius of gyration Rg (electron density) rg_electron80.08 Å
Forward intensity I(0) i01752730000.00
Molecular weight molecular_weight358350.0 kDa
Excluded volume excluded_volume449730 ų
Envelope volume envelope_volume681550 ų
Hydration-shell volume shell_volume77662 ų
Envelope diameter envelope_diameter277.1 Å
Shell Rg shell_rg62.30 Å
Envelope Rg envelope_rg79.20 Å
Shape Rg shape_rg80.08 Å
Total Rg total_rg79.78 Å
Total atoms total_atoms25239
Residues n_residues3154
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 dmax224.3 Å
Rg (real space) rg_real76.71 Å
Rg uncertainty (real space) rg_real_error1.67 Å
I(0) (real space) i0_real1.7240e+09
I(0) uncertainty (real space) i0_real_error3.7010e+07
Rg (reciprocal space) rg_reciprocal74.01 Å
I(0) (reciprocal space) i0_reciprocal1731000000.0000
Solution quality estimate total_estimate0.4868
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.9 Å
Skewness Skewness skewness0.465
Kurtosis Kurtosis kurtosis-0.868
Angular range angular_range— – 0.1000 Å−1
Current regularization parameter α current_alpha0.0603
Highest regularization parameter α highest_alpha38570000.0000
Real-space data points n_real_points21
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.523; Stabil: 0.974; Sysdev: 0.002; Positv: 1.000; Valcen: 0.587; Smooth: 0.044
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id3f3fA01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3f3fB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3f3fC01
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily500 —
Domain ID domain_id3f3fD01
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily500 —
Domain ID domain_id3f3fE01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3f3fF01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3f3fH01
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily500 —
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8. Citations (1)

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9. Files and Curves (10)