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3bg1

Architecture of a Coat for the Nuclear Pore Membrane

Method: X-RAY DIFFRACTION Dmax: 220.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein SEC13 homolog

Homo sapiens

UniProt P55735

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–316 Chain D； UniProt 1–316 Chain E； UniProt 1–316 Chain H； UniProt 1–316 Not recorded Nucleoporin NUP145 × 4 （P49687） 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
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–316 Chain D； UniProt 1–316 Not recorded Nucleoporin NUP145 × 2 （P49687） 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 1–316 Chain H； UniProt 1–316 Not recorded Nucleoporin NUP145 × 2 （P49687） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–316 Not recorded Nucleoporin NUP145 × 1 （P49687） 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
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 1–316 Not recorded Nucleoporin NUP145 × 1 （P49687） 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
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 1–316 Not recorded Nucleoporin NUP145 × 1 （P49687） 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
7 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 1–316 Not recorded Nucleoporin NUP145 × 1 （P49687） 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

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 3BG1 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–316（316 aa）
Chain D 1–316（316 aa）
Chain E 1–316（316 aa）
Chain H 1–316（316 aa）
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 structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–316（316 aa）
Chain D 1–316（316 aa）
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 structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–316（316 aa）
Chain H 1–316（316 aa）
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 structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–316（316 aa）
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 structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–316（316 aa）
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 structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–316（316 aa）
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 structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–316（316 aa）
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
5A9Q Human nuclear pore complex Deposited 2015-07-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 304 PDB declaration: 304-meric
Chain 6 1–322（322 aa）
Chain F 1–322（322 aa）
Chain O 1–322（322 aa）
Chain X 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS, 0.2-0.4% TREHALOSE；pH 7.5；20MM TRIS, 0.2-0.4% TREHALOSE
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER,
Resolution 23.00 Å
7PEQ Model of the outer rings of the human nuclear pore complex Deposited 2021-08-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 288 PDB declaration: 288-meric
Chain AF 1–322（322 aa）
Chain BF 1–322（322 aa）
Chain CF 1–322（322 aa）
Chain DF 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane.
Resolution 35.00 Å
7R5J Human nuclear pore complex (dilated) Deposited 2022-02-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain N0 1–322（322 aa）
Chain N1 1–322（322 aa）
Chain N2 1–322（322 aa）
Chain N3 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 50.00 Å
7R5K Human nuclear pore complex (constricted) Deposited 2022-02-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain N0 1–322（322 aa）
Chain N1 1–322（322 aa）
Chain N2 1–322（322 aa）
Chain N3 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.00 Å
7UHY Human GATOR2 complex Deposited 2022-03-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain H 1–322（322 aa）
Not recorded ZN ZINC ION × 32 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
7UHY Human GATOR2 complex Deposited 2022-03-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–322（322 aa）
Not recorded ZN ZINC ION × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
7UHY Human GATOR2 complex Deposited 2022-03-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–322（322 aa）
Not recorded ZN ZINC ION × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9LVJ Cryo-EM structure of Sestrin2 bound human GATOR2 complex Deposited 2025-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain H 1–368（368 aa）
Chain R 1–368（368 aa）
Not recorded ZN ZINC ION × 32 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9LVK Cryo-EM structure of CASTOR1 bound human GATOR2 complex Deposited 2025-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain H 1–368（368 aa）
Chain R 1–368（368 aa）
Not recorded ZN ZINC ION × 31 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9LWF Cryo-EM structure of dual sensor bound GATOR2 complex Deposited 2025-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain H 1–368（368 aa）
Chain R 1–368（368 aa）
Not recorded ZN ZINC ION × 32 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å
9OTI GATOR2 complex bound to arginine sensor CASTOR1 Deposited 2025-05-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain H 1–322（322 aa）
Chain R 1–322（322 aa）
Not recorded ZN ZINC ION × 29 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

10 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SEC13_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–316； UniProt 1–316 Author chain D； PDBConstruct 1–316； UniProt 1–316 Author chain E； PDBConstruct 1–316； UniProt 1–316 Author chain H； PDBConstruct 1–316； UniProt 1–316

Nucleoporin NUP145

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain B； UniProt 731–1158 Chain C； UniProt 731–1158 Chain F； UniProt 731–1158 Chain G； UniProt 731–1158 Fragment：Nucleoporin NUP145C Protein SEC13 homolog × 4 （P55735） 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
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 731–1158 Chain C； UniProt 731–1158 Fragment：Nucleoporin NUP145C Protein SEC13 homolog × 2 （P55735） 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain F； UniProt 731–1158 Chain G； UniProt 731–1158 Fragment：Nucleoporin NUP145C Protein SEC13 homolog × 2 （P55735） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 731–1158 Fragment：Nucleoporin NUP145C Protein SEC13 homolog × 1 （P55735） 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
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 731–1158 Fragment：Nucleoporin NUP145C Protein SEC13 homolog × 1 （P55735） 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
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 731–1158 Fragment：Nucleoporin NUP145C Protein SEC13 homolog × 1 （P55735） 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
7 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 731–1158 Fragment：Nucleoporin NUP145C Protein SEC13 homolog × 1 （P55735） 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

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 3BG1 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 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 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 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 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 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 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 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
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06 Different construct 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 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 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
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 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 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 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 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 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 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 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 24 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 C； PDBConstruct 15–442； UniProt 731–1158 Author chain F； PDBConstruct 15–442； UniProt 731–1158 Author chain G； PDBConstruct 15–442； UniProt 731–1158

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 3bg1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bg1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bg1
Deposition date deposition_date2007-11-23
Structure title titleArchitecture of a Coat for the Nuclear Pore Membrane
Keywords keywords;NPC, Transport, WD repeat, Autocatalytic cleavage, mRNA transport, Nuclear pore complex, Nucleus, Phosphoprotein, RNA-binding, Translocation, PROTEIN TRANSPORT, HYDROLASE ;; PROTEIN TRANSPORT, HYDROLASE
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_guinier79.98 Å
Radius of gyration Rg (electron density) rg_electron81.78 Å
Forward intensity I(0) i01448310000.00
Molecular weight molecular_weight320650.0 kDa
Excluded volume excluded_volume401810 ų
Envelope volume envelope_volume632040 ų
Hydration-shell volume shell_volume80485 ų
Envelope diameter envelope_diameter295.6 Å
Shell Rg shell_rg54.18 Å
Envelope Rg envelope_rg82.35 Å
Shape Rg shape_rg81.79 Å
Total Rg total_rg81.08 Å
Total atoms total_atoms22614
Residues n_residues2822
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 dmax220.7 Å
Rg (real space) rg_real73.31 Å
Rg uncertainty (real space) rg_real_error1.51 Å
I(0) (real space) i0_real1.3940e+09
I(0) uncertainty (real space) i0_real_error3.2300e+07
Rg (reciprocal space) rg_reciprocal74.13 Å
I(0) (reciprocal space) i0_reciprocal1426000000.0000
Solution quality estimate total_estimate0.8674
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.1 Å
Skewness Skewness skewness0.426
Kurtosis Kurtosis kurtosis-0.696
Angular range angular_range— – 0.1000 Å−1
Current regularization parameter α current_alpha0.0915
Highest regularization parameter α highest_alpha26870000.0000
Real-space data points n_real_points21
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.005; Oscil: 0.848; Stabil: 0.975; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.048
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id3bg1A00
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_id3bg1B01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily170 —
Domain ID domain_id3bg1B03
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily690 —
Domain ID domain_id3bg1C01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily170 —
Domain ID domain_id3bg1C03
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily690 —
Domain ID domain_id3bg1D00
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_id3bg1E00
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_id3bg1F01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily170 —
Domain ID domain_id3bg1F03
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily690 —
Domain ID domain_id3bg1G01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily170 —
Domain ID domain_id3bg1G03
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily690 —
Domain ID domain_id3bg1H00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
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8. Citations (1)

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9. Files and Curves (10)