SAXSdb — 6x08

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

Nucleoporin SEH1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1–349	Not recorded	Nucleoporin NUP85 × 1 （P46673） VHH-SAN2 × 1	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

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 6X08	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 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 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
3F3F Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21 Deposited 2008-10-30	Different construct Different mutation/modification Different oligomeric state 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；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
3F3G Crystal structure of the nucleoporin pair Nup85-Seh1, space group P212121 Deposited 2008-10-30	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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
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 5–353； UniProt 1–349

Nucleoporin NUP85

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–564	Not recorded	Nucleoporin SEH1 × 1 （P53011） VHH-SAN2 × 1	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

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 6X08	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 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 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
3F3F Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21 Deposited 2008-10-30	Different construct Different mutation/modification Different oligomeric state 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；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
3F3G Crystal structure of the nucleoporin pair Nup85-Seh1, space group P212121 Deposited 2008-10-30	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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
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 B； PDBConstruct 5–568； UniProt 1–564

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6x08
Deposition date deposition_date	2020-05-15
Structure title title	Nup85-Seh1 from S. cerevisiae bound by VHH-SAN2
Keywords keywords	Nucleoporin, nanobody, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	37.02 Å
Radius of gyration Rg (electron density) rg_electron	36.67 Å
Forward intensity I(0) i0	147366000.00
Molecular weight molecular_weight	96836.0 kDa
Excluded volume excluded_volume	120580 Å³
Envelope volume envelope_volume	167060 Å³
Hydration-shell volume shell_volume	39408 Å³
Envelope diameter envelope_diameter	122.8 Å
Shell Rg shell_rg	41.08 Å
Envelope Rg envelope_rg	36.45 Å
Shape Rg shape_rg	36.66 Å
Total Rg total_rg	37.00 Å
Total atoms total_atoms	6827
Residues n_residues	910
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	122.3 Å
Rg (real space) rg_real	37.30 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	1.4740e+08
I(0) uncertainty (real space) i0_real_error	2.3330e+06
Rg (reciprocal space) rg_reciprocal	37.13 Å
I(0) (reciprocal space) i0_reciprocal	147300000.0000
Solution quality estimate total_estimate	0.8322
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.1 Å
Skewness Skewness skewness	0.426
Kurtosis Kurtosis kurtosis	-0.654
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31080000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.749; Smooth: 0.760

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Nucleoporin SEH1
Molecular weight formula_weight	39469.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6827

GPGSMQPFDSGHDDLVHDVVYDFYGRHVATCSSDQHIKVFKLDKDTSNWELSDSWRAHDSSIVAIDWASPEYGRIIASASYDKTVKLWEEDPDQEECSGRRWNKLCTLNDSKGSLYSVKFAPAHLGLKLACLGNDGILRLYDALEPSDLRSWTLTSEMKVLSIPPANHLQSDFCLSWCPSRFSPEKLAVSALEQAIIYQRGKDGKLHVAAKLPGHKSLIRSISWAPSIGRWYQLIATGCKDGRIRIFKITEKLSPLASEESLTNSNMFDNSADVDMDAQGRSDSNTEEKAELQSNLQVELLSEHDDHNGEVWSVSWNLTGTILSSAGDDGKVRLWKATYSNEFKCMSVITAQQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nucleoporin NUP85
Molecular weight formula_weight	64622.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MADPMTIDDSNRLLMDVDQFDFLDDGTAQLSNNKTDEEEQLYKRDPVSGAILVPMTVNDQPIEKNGDKMPLKFKLGPLSYQNMAFITAKDKYKLYPVRIPRLDTSKEFSAYVSGLFEIYRDLGDDRVFNVPTIGVVNSNFAKEHNATVNLAMEAILNELEVFIGRVKDQDGRVNRFYELEESLTVLNCLRTMYFILDGQDVEENRSEFIESLLNWINRSDGEPDEEYIEQVFSVKDSTAGKKVFETQYFWKLLNQLVLRGLLSQAIGCIERSDLLPYLSDTCAVSFDAVSDSIELLKQYPKDSSSTFREWKNLVLKLSQAFGSSATDISGELRDYIEDFLLVIGGNQRKILQYSRTWYESFCGFLLYYIPSLELSAEYLQMSLEANVVDITNDWEQPCVDIISGKIHSILPVMESLDSCTAAFTAMICEAKGLIENIFEGEKNSDDYSNEDNEMLEDLFSYRNGMASYMLNSFAFELCSLGDKELWPVAIGLIALSATGTRSAKKMVIAELLPHYPFVTNDDIEWMLSICVEWRLPEIAKEIYTTLGNQMLSAHNIIESIANFSRAGK

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	VHH-SAN2
Molecular weight formula_weight	13517.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

QVQLVETGGGLVQPGGSLRLSCAASGFTLDDYAIGWFRQAPGKEREGVSCISRSGGSTTYTDSVKGRFTISRDNAENTVYLQMNSLKPEDTAVYYCAAARTRGTCWLNRIGMDYWGKGTQVTVSS

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	233.992 Å
Unit-cell length b length_b	233.992 Å
Unit-cell length c length_c	139.424 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	hexagonal

Resolution resolution	4.190 Å
Low-resolution limit resolution_low	117.000 Å
R factor r_factor	0.3131
R_work r_work	0.3109
R_free r_free	0.3465

fit	/app/data/saxs_computation/x0/6x08/6x08.fit
pddf	/app/data/pr_computation/x0/6x08/6x08.pr.out
profile	/app/data/saxs_computation/x0/6x08/6x08.dat

Nup85-Seh1 from S. cerevisiae bound by VHH-SAN2

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

Nucleoporin SEH1

State in the Current Structure

Other States of the Same Protein in the Database

Nucleoporin NUP85

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)