← Back to search
7wot

Cryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore complex

Method: ELECTRON MICROSCOPY Dmax: 274.2 Å Quality: EXCELLENT
▼

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

Nucleoporin NIC96

OrganismNot specified

UniProt P34077

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain A； UniProt 1–839 Chain M； UniProt 1–839 Chain N； UniProt 1–839 Chain Z； UniProt 1–839 Not recorded Nucleoporin NUP157 × 2 （P40064） Nucleoporin NUP170 × 2 （P38181） Nucleoporin NUP188 × 2 （P52593） Nucleoporin NUP192 × 2 （P47054） Nucleoporin NUP49/NSP49 × 4 （Q02199） Nucleoporin NUP57 × 4 （P48837） Nucleoporin NSP1 × 4 （P14907） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.73 Å

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 7WOT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2QX5 Structure of nucleoporin Nic96 Deposited 2007-08-10 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 186–839（654 aa） Fragment：residues 186-839
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Potassium Thiocyanate, 1mM Cetyltrimethylammonium bromide, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.285
2QX5 Structure of nucleoporin Nic96 Deposited 2007-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 186–839（654 aa） Fragment：residues 186-839
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Potassium Thiocyanate, 1mM Cetyltrimethylammonium bromide, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.285
2RFO Crystral Structure of the nucleoporin Nic96 Deposited 2007-10-01 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 189–839（651 aa） Fragment：UNP residues 189-839
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；3-10% PEG3350, 0.1M BisTris pH6.5, 0.05M lithium sulfate, 3% 1,6-hexandiole, 0.01mM DTE, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.285
2RFO Crystral Structure of the nucleoporin Nic96 Deposited 2007-10-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 189–839（651 aa） Fragment：UNP residues 189-839
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；3-10% PEG3350, 0.1M BisTris pH6.5, 0.05M lithium sulfate, 3% 1,6-hexandiole, 0.01mM DTE, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.285
6X07 Nic96 from S. cerevisiae bound by VHH-SAN12 Deposited 2020-05-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 186–839（654 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；8% PEG 8,000 and 0.1M tri-sodium citrate pH 5
Resolution 2.10 Å R-free 0.245
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain Q 1–839（839 aa）
Chain R 1–839（839 aa）
Chain S 1–839（839 aa）
Chain T 1–839（839 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain Q 1–839（839 aa）
Chain R 1–839（839 aa）
Chain S 1–839（839 aa）
Chain T 1–839（839 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain Q 1–839（839 aa）
Chain R 1–839（839 aa）
Chain S 1–839（839 aa）
Chain T 1–839（839 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain Q 1–839（839 aa）
Chain R 1–839（839 aa）
Chain S 1–839（839 aa）
Chain T 1–839（839 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain Q 1–839（839 aa）
Chain R 1–839（839 aa）
Chain S 1–839（839 aa）
Chain T 1–839（839 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain Q 1–839（839 aa）
Chain R 1–839（839 aa）
Chain S 1–839（839 aa）
Chain T 1–839（839 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
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–839（839 aa）
Chain Z 1–839（839 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain Q 1–839（839 aa）
Chain R 1–839（839 aa）
Chain S 1–839（839 aa）
Chain T 1–839（839 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 6.60 Å

7 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NIC96_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–839； UniProt 1–839 Author chain M； PDBConstruct 1–839； UniProt 1–839 Author chain N； PDBConstruct 1–839； UniProt 1–839 Author chain Z； PDBConstruct 1–839； UniProt 1–839

Nucleoporin NUP157

OrganismNot specified

UniProt P40064

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain C； UniProt 1–1391 Chain O； UniProt 1–1391 Not recorded Nucleoporin NIC96 × 4 （P34077） Nucleoporin NUP170 × 2 （P38181） Nucleoporin NUP188 × 2 （P52593） Nucleoporin NUP192 × 2 （P47054） Nucleoporin NUP49/NSP49 × 4 （Q02199） Nucleoporin NUP57 × 4 （P48837） Nucleoporin NSP1 × 4 （P14907） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.73 Å

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 7WOT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4MHC Crystal Structure of a Nucleoporin Deposited 2013-08-29 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 70–893（824 aa） Fragment：N-terminal domain (UNP residues 70-893)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；5% PEG 4,000, 0.1 M MES, pH 6.0, 0.05 M Magnesium chloride, 3% (v/v) 1,4-dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.231
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain 1 1–1391（1391 aa）
Chain Z 1–1391（1391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 1 1–1391（1391 aa）
Chain Z 1–1391（1391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 1 1–1391（1391 aa）
Chain Z 1–1391（1391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain 1 1–1391（1391 aa）
Chain Z 1–1391（1391 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain 1 1–1391（1391 aa）
Chain Z 1–1391（1391 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain 1 1–1391（1391 aa）
Chain Z 1–1391（1391 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
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–1391（1391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain 1 1–1391（1391 aa）
Chain Z 1–1391（1391 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 6.60 Å

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

View Construct and Data Evidence
UniProt name NU157_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–1391； UniProt 1–1391 Author chain O； PDBConstruct 1–1391； UniProt 1–1391

Nucleoporin NUP170

OrganismNot specified

UniProt P38181

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain D； UniProt 1–1502 Chain P； UniProt 1–1502 Not recorded Nucleoporin NIC96 × 4 （P34077） Nucleoporin NUP157 × 2 （P40064） Nucleoporin NUP188 × 2 （P52593） Nucleoporin NUP192 × 2 （P47054） Nucleoporin NUP49/NSP49 × 4 （Q02199） Nucleoporin NUP57 × 4 （P48837） Nucleoporin NSP1 × 4 （P14907） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.73 Å

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 7WOT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3I5P Nup170(aa979-1502), S.cerevisiae Deposited 2009-07-06 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 980–1502（523 aa） Fragment：HELICAL DOMAIN (UNP residues 980-1502)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, 8% PEG 3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.20 Å R-free 0.324
3I5Q Nup170(aa1253-1502) at 2.2 A, S.cerevisiae Deposited 2009-07-06 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 B 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M LITHIUM SULFATE, 0.1M TRIS-HCL, 50 mM NACL, 22% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.20 Å R-free 0.272
3I5Q Nup170(aa1253-1502) at 2.2 A, S.cerevisiae Deposited 2009-07-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M LITHIUM SULFATE, 0.1M TRIS-HCL, 50 mM NACL, 22% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.20 Å R-free 0.272
3I5Q Nup170(aa1253-1502) at 2.2 A, S.cerevisiae Deposited 2009-07-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)
Chain B 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M LITHIUM SULFATE, 0.1M TRIS-HCL, 50 mM NACL, 22% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.20 Å R-free 0.272
3I5Q Nup170(aa1253-1502) at 2.2 A, S.cerevisiae Deposited 2009-07-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)
Chain B 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M LITHIUM SULFATE, 0.1M TRIS-HCL, 50 mM NACL, 22% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.20 Å R-free 0.272
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–1502（1502 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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 6.60 Å

6 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NU170_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–1502； UniProt 1–1502 Author chain P； PDBConstruct 1–1502； UniProt 1–1502

Nucleoporin NUP188

OrganismNot specified

UniProt P52593

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain E； UniProt 1–1655 Chain Q； UniProt 1–1655 Not recorded Nucleoporin NIC96 × 4 （P34077） Nucleoporin NUP157 × 2 （P40064） Nucleoporin NUP170 × 2 （P38181） Nucleoporin NUP192 × 2 （P47054） Nucleoporin NUP49/NSP49 × 4 （Q02199） Nucleoporin NUP57 × 4 （P48837） Nucleoporin NSP1 × 4 （P14907） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.73 Å

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 7WOT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 136 PDB declaration: 136-meric
Chain X 1–1655（1655 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 structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain X 1–1655（1655 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 structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain X 1–1655（1655 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
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain N 1–1655（1655 aa）
Chain P 1–1655（1655 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain N 1–1655（1655 aa）
Chain P 1–1655（1655 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain N 1–1655（1655 aa）
Chain P 1–1655（1655 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain N 1–1655（1655 aa）
Chain P 1–1655（1655 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain N 1–1655（1655 aa）
Chain P 1–1655（1655 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain N 1–1655（1655 aa）
Chain P 1–1655（1655 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
7WO9 Cryo-EM structure of full-length Nup188 Deposited 2022-01-20 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1655（1655 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–1655（1655 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain N 1–1655（1655 aa）
Chain P 1–1655（1655 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 6.60 Å

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

View Construct and Data Evidence
UniProt name NU188_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–1655； UniProt 1–1655 Author chain Q； PDBConstruct 1–1655； UniProt 1–1655

Nucleoporin NUP192

OrganismNot specified

UniProt P47054

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain F； UniProt 1–1683 Chain R； UniProt 1–1683 Not recorded Nucleoporin NIC96 × 4 （P34077） Nucleoporin NUP157 × 2 （P40064） Nucleoporin NUP170 × 2 （P38181） Nucleoporin NUP188 × 2 （P52593） Nucleoporin NUP49/NSP49 × 4 （Q02199） Nucleoporin NUP57 × 4 （P48837） Nucleoporin NSP1 × 4 （P14907） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.73 Å

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 7WOT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4IFQ Crystal structure of Saccharomyces cerevisiae NUP192, residues 2 to 960 [ScNup192(2-960)] Deposited 2012-12-14 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 2–960（959 aa） Fragment：UNP residues 2-960
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 7 IOD IODIDE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Protein (20 mM Hepes, pH 8.0, 500 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (10% PEG3350, 100mM pottasium iodide); Cryoprotection (30% PEG400 and 25% saturated ammonium sulfate), Vapor Diffusion, Sitting Drop, temperature 298K
Resolution 3.25 Å R-free 0.243
4IFQ Crystal structure of Saccharomyces cerevisiae NUP192, residues 2 to 960 [ScNup192(2-960)] Deposited 2012-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–960（959 aa） Fragment：UNP residues 2-960
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 14 IOD IODIDE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Protein (20 mM Hepes, pH 8.0, 500 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (10% PEG3350, 100mM pottasium iodide); Cryoprotection (30% PEG400 and 25% saturated ammonium sulfate), Vapor Diffusion, Sitting Drop, temperature 298K
Resolution 3.25 Å R-free 0.243
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 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
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–1683（1683 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 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 6.60 Å

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NU192_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 1–1683； UniProt 1–1683 Author chain R； PDBConstruct 1–1683； UniProt 1–1683

Nucleoporin NUP49/NSP49

OrganismNot specified

UniProt Q02199

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain G； UniProt 1–472 Chain J； UniProt 1–472 Chain S； UniProt 1–472 Chain V； UniProt 1–472 Not recorded Nucleoporin NIC96 × 4 （P34077） Nucleoporin NUP157 × 2 （P40064） Nucleoporin NUP170 × 2 （P38181） Nucleoporin NUP188 × 2 （P52593） Nucleoporin NUP192 × 2 （P47054） Nucleoporin NUP57 × 4 （P48837） Nucleoporin NSP1 × 4 （P14907） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.73 Å

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 7WOT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain C 1–472（472 aa）
Chain F 1–472（472 aa）
Chain I 1–472（472 aa）
Chain L 1–472（472 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain C 1–472（472 aa）
Chain F 1–472（472 aa）
Chain I 1–472（472 aa）
Chain L 1–472（472 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain C 1–472（472 aa）
Chain F 1–472（472 aa）
Chain I 1–472（472 aa）
Chain L 1–472（472 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain C 1–472（472 aa）
Chain F 1–472（472 aa）
Chain I 1–472（472 aa）
Chain L 1–472（472 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain C 1–472（472 aa）
Chain F 1–472（472 aa）
Chain I 1–472（472 aa）
Chain L 1–472（472 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain C 1–472（472 aa）
Chain F 1–472（472 aa）
Chain I 1–472（472 aa）
Chain L 1–472（472 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
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–472（472 aa）
Chain J 1–472（472 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain C 1–472（472 aa）
Chain F 1–472（472 aa）
Chain I 1–472（472 aa）
Chain L 1–472（472 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 6.60 Å

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

View Construct and Data Evidence
UniProt name NUP49_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain G； PDBConstruct 1–472； UniProt 1–472 Author chain J； PDBConstruct 1–472； UniProt 1–472 Author chain S； PDBConstruct 1–472； UniProt 1–472 Author chain V； PDBConstruct 1–472； UniProt 1–472

Nucleoporin NUP57

OrganismNot specified

UniProt P48837

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain H； UniProt 1–541 Chain K； UniProt 1–541 Chain T； UniProt 1–541 Chain W； UniProt 1–541 Not recorded Nucleoporin NIC96 × 4 （P34077） Nucleoporin NUP157 × 2 （P40064） Nucleoporin NUP170 × 2 （P38181） Nucleoporin NUP188 × 2 （P52593） Nucleoporin NUP192 × 2 （P47054） Nucleoporin NUP49/NSP49 × 4 （Q02199） Nucleoporin NSP1 × 4 （P14907） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.73 Å

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 7WOT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain B 1–541（541 aa）
Chain E 1–541（541 aa）
Chain H 1–541（541 aa）
Chain K 1–541（541 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain B 1–541（541 aa）
Chain E 1–541（541 aa）
Chain H 1–541（541 aa）
Chain K 1–541（541 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain B 1–541（541 aa）
Chain E 1–541（541 aa）
Chain H 1–541（541 aa）
Chain K 1–541（541 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain B 1–541（541 aa）
Chain E 1–541（541 aa）
Chain H 1–541（541 aa）
Chain K 1–541（541 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain B 1–541（541 aa）
Chain E 1–541（541 aa）
Chain H 1–541（541 aa）
Chain K 1–541（541 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain B 1–541（541 aa）
Chain E 1–541（541 aa）
Chain H 1–541（541 aa）
Chain K 1–541（541 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
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–541（541 aa）
Chain K 1–541（541 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain B 1–541（541 aa）
Chain E 1–541（541 aa）
Chain H 1–541（541 aa）
Chain K 1–541（541 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 6.60 Å

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

View Construct and Data Evidence
UniProt name NUP57_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain H； PDBConstruct 1–541； UniProt 1–541 Author chain K； PDBConstruct 1–541； UniProt 1–541 Author chain T； PDBConstruct 1–541； UniProt 1–541 Author chain W； PDBConstruct 1–541； UniProt 1–541

Nucleoporin NSP1

OrganismNot specified

UniProt P14907

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain I； UniProt 1–823 Chain L； UniProt 1–823 Chain U； UniProt 1–823 Chain X； UniProt 1–823 Not recorded Nucleoporin NIC96 × 4 （P34077） Nucleoporin NUP157 × 2 （P40064） Nucleoporin NUP170 × 2 （P38181） Nucleoporin NUP188 × 2 （P52593） Nucleoporin NUP192 × 2 （P47054） Nucleoporin NUP49/NSP49 × 4 （Q02199） Nucleoporin NUP57 × 4 （P48837） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.73 Å

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 7WOT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1O6O Importin Beta aa1-442 bound to five FxFG repeats from yeast Nsp1p. Second crystal form Deposited 2002-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 497–608（112 aa） Fragment：RESIDUES 497-608
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.9；1.2-1.28M AMMONIUM SULPHATE, 100MM AMMONIUM ACETATE, PH 5.9, 30MM DTT
Resolution 2.80 Å R-free 0.273
1O6O Importin Beta aa1-442 bound to five FxFG repeats from yeast Nsp1p. Second crystal form Deposited 2002-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 497–608（112 aa） Fragment：RESIDUES 497-608
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.9；1.2-1.28M AMMONIUM SULPHATE, 100MM AMMONIUM ACETATE, PH 5.9, 30MM DTT
Resolution 2.80 Å R-free 0.273
1O6O Importin Beta aa1-442 bound to five FxFG repeats from yeast Nsp1p. Second crystal form Deposited 2002-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 497–608（112 aa） Fragment：RESIDUES 497-608
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.9；1.2-1.28M AMMONIUM SULPHATE, 100MM AMMONIUM ACETATE, PH 5.9, 30MM DTT
Resolution 2.80 Å R-free 0.273
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain A 1–823（823 aa）
Chain D 1–823（823 aa）
Chain G 1–823（823 aa）
Chain J 1–823（823 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 1–823（823 aa）
Chain D 1–823（823 aa）
Chain G 1–823（823 aa）
Chain J 1–823（823 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different oligomeric state Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 1–823（823 aa）
Chain D 1–823（823 aa）
Chain G 1–823（823 aa）
Chain J 1–823（823 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain A 1–823（823 aa）
Chain D 1–823（823 aa）
Chain G 1–823（823 aa）
Chain J 1–823（823 aa）
Chain y 1–823（823 aa）
Chain z 1–823（823 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 conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain A 1–823（823 aa）
Chain D 1–823（823 aa）
Chain G 1–823（823 aa）
Chain J 1–823（823 aa）
Chain y 1–823（823 aa）
Chain z 1–823（823 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 conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain A 1–823（823 aa）
Chain D 1–823（823 aa）
Chain G 1–823（823 aa）
Chain J 1–823（823 aa）
Chain y 1–823（823 aa）
Chain z 1–823（823 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
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 1–823（823 aa）
Chain L 1–823（823 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain A 1–823（823 aa）
Chain D 1–823（823 aa）
Chain G 1–823（823 aa）
Chain J 1–823（823 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 6.60 Å

5 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NSP1_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain I； PDBConstruct 1–823； UniProt 1–823 Author chain L； PDBConstruct 1–823； UniProt 1–823 Author chain U； PDBConstruct 1–823； UniProt 1–823 Author chain X； PDBConstruct 1–823； UniProt 1–823

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 7wot

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7wot
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id7wot
Deposition date deposition_date2022-01-22
Structure title titleCryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore complex
Keywords keywordsnuclear pore complex, inner ring, monomer, Saccharomyces cerevisiae, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier— Å
Radius of gyration Rg (electron density) rg_electron105.30 Å
Forward intensity I(0) i047132400000.00
Molecular weight molecular_weight1896100.0 kDa
Excluded volume excluded_volume2388000 ų
Envelope volume envelope_volume4895400 ų
Hydration-shell volume shell_volume387940 ų
Envelope diameter envelope_diameter407.1 Å
Shell Rg shell_rg105.70 Å
Envelope Rg envelope_rg100.00 Å
Shape Rg shape_rg105.30 Å
Total Rg total_rg105.40 Å
Total atoms total_atoms133827
Residues n_residues17285
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax274.2 Å
Rg (real space) rg_real100.70 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real4.4830e+10
I(0) uncertainty (real space) i0_real_error8.5150e+08
Rg (reciprocal space) rg_reciprocal106.90 Å
I(0) (reciprocal space) i0_reciprocal47390000000.0000
Solution quality estimate total_estimate0.9075
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary127.9 Å
Skewness Skewness skewness0.075
Kurtosis Kurtosis kurtosis-0.505
Angular range angular_range— – 0.0750 Å−1
Current regularization parameter α current_alpha0.8603
Highest regularization parameter α highest_alpha3535000000.0000
Real-space data points n_real_points16
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.002; Oscil: 0.996; Stabil: 0.964; Sysdev: 1.000; Positv: 1.000; Valcen: 0.919; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (8)

▶

8. Citations (1)

▶

9. Files and Curves (10)