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3iko

Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex

Method: X-RAY DIFFRACTION Dmax: 229.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein transport protein SEC13

Saccharomyces cerevisiae

UniProt Q04491

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 1–297 Fragment：UNP residues 1-297 Nucleoporin NUP145C × 1 （P49687） Nucleoporin NUP84 × 1 （P52891） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 1–297 Fragment：UNP residues 1-297 Nucleoporin NUP145C × 1 （P49687） Nucleoporin NUP84 × 1 （P52891） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.273
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain G； UniProt 1–297 Fragment：UNP residues 1-297 Nucleoporin NUP145C × 1 （P49687） Nucleoporin NUP84 × 1 （P52891） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.273

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 3IKO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2PM6 Crystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native version Deposited 2007-04-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–297（297 aa）
Chain D 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15% PEG 4000, 10% DMSO, 6% dioxanie, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.45 Å R-free 0.301
2PM7 Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat, selenomethionine version Deposited 2007-04-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–297（297 aa）
Chain D 1–297（297 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 7.5；277 K；15% PEG 4000, 10% DMSO, 6% dioxane, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.35 Å R-free 0.298
2PM9 Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat Deposited 2007-04-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；8% PEG 3350, 0.1M tri-sodium citrate, 10mM manganese chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.30 Å R-free 0.305
3JRO NUP84-NUP145C-SEC13 edge element of the NPC lattice Deposited 2009-09-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–297（297 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；pH 5.7；295 K；1.15M sodium malonate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 4.00 Å R-free 0.329
3JRP SEC13 with NUP145C (AA109-179) insertion blade Deposited 2009-09-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；289 K；0.1M Tris, 22% PEG 4000, 0.25 M LiCl, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.60 Å R-free 0.254
3MZK Sec13/Sec16 complex, S.cerevisiae Deposited 2010-05-12 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 1–297（297 aa）
Chain D 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1mM bis-Tris propane, 0.2M NaBr, 12% polyethylene glycol 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.69 Å R-free 0.243
3MZL Sec13/Sec31 edge element, loop deletion mutant Deposited 2010-05-12 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 1–297（297 aa）
Chain C 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；289 K；0.1mM bis-Tris propane, 0.2M sodium citrate, 16% polyethylene glycol 3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.80 Å R-free 0.300
3MZL Sec13/Sec31 edge element, loop deletion mutant Deposited 2010-05-12 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 1–297（297 aa）
Chain G 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；289 K；0.1mM bis-Tris propane, 0.2M sodium citrate, 16% polyethylene glycol 3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.80 Å R-free 0.300
4BZJ The structure of the COPII coat assembled on membranes Deposited 2013-07-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–292（291 aa）
Chain F 2–292（291 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer HEPES, 50 MM KOAC, 1.2 MM MGCL2；pH 6.8；HEPES, 50 MM KOAC, 1.2 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；ETHANE; HOMEMADE PLUNGER
Resolution 40.00 Å
4BZK The structure of the COPII coat assembled on membranes Deposited 2013-07-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–297（297 aa）
Chain F 1–297（297 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer HEPES, 50 MM KOAC, 1.2 MM MGCL2；pH 6.8；HEPES, 50 MM KOAC, 1.2 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；ETHANE; HOMEMADE PLUNGER
Resolution 40.00 Å
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 A 1–297（297 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 A 2–297（296 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
6ZG5 COPII on membranes, outer coat right-handed rod, class1 Deposited 2020-06-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–297（297 aa）
Chain F 1–297（297 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 40.00 Å
6ZG6 COPII on membranes, outer coat vertex Deposited 2020-06-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–297（297 aa）
Chain D 1–297（297 aa）
Chain F 1–297（297 aa）
Chain H 1–297（297 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.00 Å
6ZL0 COPII on membranes, outer coat left-handed rod Deposited 2020-06-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–297（297 aa）
Chain D 1–297（297 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 40.00 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 1 Protein heterocomplex Heteromer；Protein × 136 PDB declaration: 136-meric
Chain d 1–297（297 aa）
Chain o 1–297（297 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 d 1–297（297 aa）
Chain o 1–297（297 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 d 1–297（297 aa）
Chain o 1–297（297 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 d 1–297（297 aa）
Chain k 1–297（297 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 d 1–297（297 aa）
Chain k 1–297（297 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 d 1–297（297 aa）
Chain k 1–297（297 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 H 1–297（297 aa）
Chain P 1–297（297 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
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 d 1–297（297 aa）
Chain o 1–297（297 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
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 H 1–297（297 aa）
Chain P 1–297（297 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

19 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SEC13_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–297； UniProt 1–297 Author chain D； PDBConstruct 1–297； UniProt 1–297 Author chain G； PDBConstruct 1–297； UniProt 1–297

Nucleoporin NUP145C

Saccharomyces cerevisiae

UniProt P49687

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 731–1158 Fragment：UNP residues 731-1158 Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP84 × 1 （P52891） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain E； UniProt 731–1158 Fragment：UNP residues 731-1158 Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP84 × 1 （P52891） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.273
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain H； UniProt 731–1158 Fragment：UNP residues 731-1158 Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP84 × 1 （P52891） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.273

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 3IKO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BG0 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 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 B 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain C 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain F 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain G 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.15 Å R-free 0.294
3BG0 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 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 B 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain C 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.15 Å R-free 0.294
3BG0 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 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 F 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain G 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.15 Å R-free 0.294
3BG0 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.15 Å R-free 0.294
3BG0 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.15 Å R-free 0.294
3BG0 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.15 Å R-free 0.294
3BG0 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.15 Å R-free 0.294
3BG1 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 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 B 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain C 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain F 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain G 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.294
3BG1 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 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 B 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain C 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.294
3BG1 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 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 F 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Chain G 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.294
3BG1 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.294
3BG1 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.294
3BG1 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.294
3BG1 Architecture of a Coat for the Nuclear Pore Membrane Deposited 2007-11-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 731–1158（428 aa） Fragment：Nucleoporin NUP145C
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；294 K；16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.294
3JRO NUP84-NUP145C-SEC13 edge element of the NPC lattice Deposited 2009-09-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 714–1160（447 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；pH 5.7；295 K；1.15M sodium malonate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 4.00 Å R-free 0.329
3JRP SEC13 with NUP145C (AA109-179) insertion blade Deposited 2009-09-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 714–784（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；289 K；0.1M Tris, 22% PEG 4000, 0.25 M LiCl, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.60 Å R-free 0.254
3KEP Crystal structure of the autoproteolytic domain from the nuclear pore complex component NUP145 from Saccharomyces cerevisiae Deposited 2009-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 442–605（164 aa） Fragment：residues 442 to 605
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；100mM HEPES, 25% PEG 3350, 200mM NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.82 Å R-free 0.244
3KEP Crystal structure of the autoproteolytic domain from the nuclear pore complex component NUP145 from Saccharomyces cerevisiae Deposited 2009-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 442–605（164 aa） Fragment：residues 442 to 605
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；100mM HEPES, 25% PEG 3350, 200mM NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.82 Å R-free 0.244
3KES Crystal structure of the autoproteolytic domain from the nuclear pore complex component NUP145 from Saccharomyces cerevisiae in the Hexagonal, P61 space group Deposited 2009-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 442–605（164 aa） Fragment：residues 442 to 605
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1600mM tri-sodium citrate dehydrate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.10 Å R-free 0.230
3KES Crystal structure of the autoproteolytic domain from the nuclear pore complex component NUP145 from Saccharomyces cerevisiae in the Hexagonal, P61 space group Deposited 2009-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 442–605（164 aa） Fragment：residues 442 to 605
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1600mM tri-sodium citrate dehydrate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.10 Å R-free 0.230
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 B 680–1317（638 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 B 680–1317（638 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 c 606–1317（712 aa）
Chain n 606–1317（712 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 c 606–1317（712 aa）
Chain n 606–1317（712 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 c 606–1317（712 aa）
Chain n 606–1317（712 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 c 606–1317（712 aa）
Chain j 606–1317（712 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 c 606–1317（712 aa）
Chain j 606–1317（712 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 c 606–1317（712 aa）
Chain j 606–1317（712 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

10 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NU145_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 15–442； UniProt 731–1158 Author chain E； PDBConstruct 15–442； UniProt 731–1158 Author chain H； PDBConstruct 15–442； UniProt 731–1158

Nucleoporin NUP84

Saccharomyces cerevisiae

UniProt P52891

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 1–460 Fragment：UNP residues 1-460 Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP145C × 1 （P49687） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain F； UniProt 1–460 Fragment：UNP residues 1-460 Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP145C × 1 （P49687） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.273
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain I； UniProt 1–460 Fragment：UNP residues 1-460 Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP145C × 1 （P49687） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.20 Å R-free 0.273

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 3IKO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JRO NUP84-NUP145C-SEC13 edge element of the NPC lattice Deposited 2009-09-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–424（424 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；pH 5.7；295 K；1.15M sodium malonate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 4.00 Å R-free 0.329
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 F 1–451（451 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 F 2–451（450 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
6X02 Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 Deposited 2020-05-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% PEG 8,000, 30% ethylene glycol, 0.1M imidazole titrated with MES pH 6.5, 15mM sodium nitrate, 15mM sodium phosphate dibasic, 15mM ammonium sulfate
Resolution 6.38 Å R-free 0.324
6X03 Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9 Deposited 2020-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–726（726 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% PEG 8,000, 30% ethylene glycol, 0.1M imidazole titrated with MES pH 6.5, 15mM sodium nitrate, 15mM sodium phosphate dibasic, 15mM ammonium sulfate
Resolution 7.30 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 f 1–726（726 aa）
Chain q 1–726（726 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 f 1–726（726 aa）
Chain q 1–726（726 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 f 1–726（726 aa）
Chain q 1–726（726 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 f 1–726（726 aa）
Chain m 1–726（726 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 f 1–726（726 aa）
Chain m 1–726（726 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 f 1–726（726 aa）
Chain m 1–726（726 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 f 1–726（726 aa）
Chain q 1–726（726 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

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

View Construct and Data Evidence
UniProt name NUP84_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–460； UniProt 1–460 Author chain F； PDBConstruct 1–460； UniProt 1–460 Author chain I； PDBConstruct 1–460； UniProt 1–460

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 3iko

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3iko
Deposition date deposition_date2009-08-06
Structure title titleCrystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex
Keywords keywords;NPC, TRANSPORT, WD REPEAT, AUTOCATALYTIC CLEAVAGE, MRNA TRANSPORT, NUCLEAR PORE COMPLEX, NUCLEUS, PHOSPHOPROTEIN, TRANSLOCATION, PROTEIN TRANSPORT, Coiled coil, Membrane, Hydrolase, RNA-binding, Cytoplasmic vesicle, Endoplasmic reticulum, ER-Golgi transport, NUCLEAR PROTEIN, STRUCTURAL PROTEIN ;; STRUCTURAL PROTEIN, PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier63.70 Å
Radius of gyration Rg (electron density) rg_electron63.72 Å
Forward intensity I(0) i01988230000.00
Molecular weight molecular_weight382870.0 kDa
Excluded volume excluded_volume482610 ų
Envelope volume envelope_volume723930 ų
Hydration-shell volume shell_volume101910 ų
Envelope diameter envelope_diameter221.6 Å
Shell Rg shell_rg57.38 Å
Envelope Rg envelope_rg63.38 Å
Shape Rg shape_rg63.75 Å
Total Rg total_rg63.44 Å
Total atoms total_atoms27032
Residues n_residues3351
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax229.3 Å
Rg (real space) rg_real63.92 Å
Rg uncertainty (real space) rg_real_error2.50 Å
I(0) (real space) i0_real1.9880e+09
I(0) uncertainty (real space) i0_real_error4.1280e+07
Rg (reciprocal space) rg_reciprocal63.50 Å
I(0) (reciprocal space) i0_reciprocal1987000000.0000
Solution quality estimate total_estimate0.8039
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary82.6 Å
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.522
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0032
Highest regularization parameter α highest_alpha96760000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id3ikoA01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3ikoB03
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily690 —
Domain ID domain_id3ikoC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3450 — Hyaluronidase domain-like
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3ikoD01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3ikoE01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily170 —
Domain ID domain_id3ikoE03
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily690 —
Domain ID domain_id3ikoF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3450 — Hyaluronidase domain-like
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3ikoG01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3ikoH01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily170 —
Domain ID domain_id3ikoH03
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily690 —
Domain ID domain_id3ikoI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3450 — Hyaluronidase domain-like
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)