SAXSdb — 3jro

▼

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

Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 714–1160	Non-standard monomer：Yes (specific site not provided by mmCIF)	Nucleoporin NUP84 × 1 （P52891）	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

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 3JRO	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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 731–1158（428 aa） Fragment：UNP residues 731-1158	Not recorded	No recorded non-water small molecule	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
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 731–1158（428 aa） Fragment：UNP residues 731-1158	Not recorded	No recorded non-water small molecule	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
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 731–1158（428 aa） Fragment：UNP residues 731-1158	Not recorded	No recorded non-water small molecule	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
3JRP SEC13 with NUP145C (AA109-179) insertion blade Deposited 2009-09-08	Different construct Different mutation/modification 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 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 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 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 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 mutation/modification 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 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 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NU145_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 307–753； UniProt 714–1160

Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145

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	Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–297	Non-standard monomer：Yes (specific site not provided by mmCIF)	Nucleoporin NUP84 × 1 （P52891）	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

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 3JRO	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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–297（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
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–297（297 aa） Fragment：UNP residues 1-297	Not recorded	No recorded non-water small molecule	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
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–297（297 aa） Fragment：UNP residues 1-297	Not recorded	No recorded non-water small molecule	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
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–297（297 aa） Fragment：UNP residues 1-297	Not recorded	No recorded non-water small molecule	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
3JRP SEC13 with NUP145C (AA109-179) insertion blade Deposited 2009-09-08	Different mutation/modification 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–297（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 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 26 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

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	Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–424	Non-standard monomer：Yes (specific site not provided by mmCIF)	Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145 × 1 （Q04491,P49687）	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

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 3JRO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–460（460 aa） Fragment：UNP residues 1-460	Not recorded	No recorded non-water small molecule	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
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–460（460 aa） Fragment：UNP residues 1-460	Not recorded	No recorded non-water small molecule	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
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–460（460 aa） Fragment：UNP residues 1-460	Not recorded	No recorded non-water small molecule	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
4XMM Structure of the yeast coat nucleoporin complex, space group C2 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 × 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 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–726（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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–726（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 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUP84_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–426； UniProt 1–424

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3jro
Deposition date deposition_date	2009-09-08
Structure title title	NUP84-NUP145C-SEC13 edge element of the NPC lattice
Keywords keywords	;PROTEIN COMPLEX, CYTOPLASMIC VESICLE, ENDOPLASMIC RETICULUM, ER-GOLGI TRANSPORT, MEMBRANE, MRNA TRANSPORT, NUCLEAR PORE COMPLEX, NUCLEUS, PROTEIN TRANSPORT, TRANSLOCATION, TRANSPORT, WD REPEAT, AUTOCATALYTIC CLEAVAGE, HYDROLASE, PHOSPHOPROTEIN, TRANSPORT PROTEIN, STRUCTURAL PROTEIN ;; TRANSPORT PROTEIN, STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	45.44 Å
Radius of gyration Rg (electron density) rg_electron	46.29 Å
Forward intensity I(0) i0	219048000.00
Molecular weight molecular_weight	123400.0 kDa
Excluded volume excluded_volume	155100 Å³
Envelope volume envelope_volume	215440 Å³
Hydration-shell volume shell_volume	42800 Å³
Envelope diameter envelope_diameter	165.3 Å
Shell Rg shell_rg	44.10 Å
Envelope Rg envelope_rg	46.69 Å
Shape Rg shape_rg	46.28 Å
Total Rg total_rg	46.24 Å
Total atoms total_atoms	8671
Residues n_residues	1068
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	154.2 Å
Rg (real space) rg_real	46.20 Å
Rg uncertainty (real space) rg_real_error	1.72 Å
I(0) (real space) i0_real	2.1900e+08
I(0) uncertainty (real space) i0_real_error	4.1040e+06
Rg (reciprocal space) rg_reciprocal	45.45 Å
I(0) (reciprocal space) i0_reciprocal	218800000.0000
Solution quality estimate total_estimate	0.6863
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.8 Å
Skewness Skewness skewness	0.569
Kurtosis Kurtosis kurtosis	-0.530
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	33560000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.480; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.294; Smooth: 0.185

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145
Molecular weight formula_weight	85364.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8671

MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQGPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQGGGGSGGGGATSKEFDGPCQNEIDLLFSECNDEIDNAKLIMKERRFTASYTFAKFSTGSMLLTKDIVGKSGVSIKRLPTELQRKFLFDDVYLDKEIEKVTIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSILFDPVSYPYKTDNDQVKMALLKKERHCRLTSWIVSQIGPEIEEKIRNSSNEIEQIFLYLLLNDVVRASKLAIESKNGHLSVLISYLGSNDPRIRDLAELQLQKWSTGGCSIDKNISKIYKLLSGSPFEGLFSLKELESEFSWLCLLNLTLCYGQIDEYSLESLVQSHLDKFSLPYDDPIGVIFQLYAANENTEKLYKEVRQRTNALDVQFCWYLIQTLRFNGTRVFSKETSDEATFAFAAQLEFAQLHGHSLFVSCFLNDDKAAEDTIKRLVMREITLLRASTNDHILNRLKIPSQLIFNAQALKDRYEGNYLSE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nucleoporin NUP84
Molecular weight formula_weight	49248.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSMELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVISSKDWELEARFWHLVELLLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLYQIWIVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDFPLRENTNVLDVKDKEEDHIFFKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGIKKHSLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTEIENYLLENNQVGTDELILPLPSHALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPSVIHSSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIINPGSVEEVDKSKLITTYISLLKLQG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3jroA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3jroC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3450 — Hyaluronidase domain-like
Homologous superfamily homologous superfamily	20 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	170.472 Å
Unit-cell length b length_b	170.472 Å
Unit-cell length c length_c	270.732 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	4.004 Å
Low-resolution limit resolution_low	49.887 Å
R factor r_factor	0.2858
R_work r_work	0.2821
R_free r_free	0.3289

fit	/app/data/saxs_computation/jr/3jro/3jro.fit
pddf	/app/data/pr_computation/jr/3jro/3jro.pr.out
profile	/app/data/saxs_computation/jr/3jro/3jro.dat

NUP84-NUP145C-SEC13 edge element of the NPC lattice

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

Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145

State in the Current Structure

Other States of the Same Protein in the Database

Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145

State in the Current Structure

Other States of the Same Protein in the Database

Nucleoporin NUP84

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)