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5ijn

Composite structure of the inner ring of the human nuclear pore complex (32 copies of Nup205)

Method: ELECTRON MICROSCOPY Dmax: 283.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NUCLEAR PORE COMPLEX PROTEIN NUP155

Homo sapiens

UniProt O75694

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 × 208 PDB declaration: 208-meric（208） Consistent with protein copy count Chain A； UniProt 1–1391 Chain B； UniProt 1–1391 Chain E； UniProt 1–1391 Chain K； UniProt 1–1391 Chain Q； UniProt 1–1391 Chain W； UniProt 1–1391 Not recorded NUCLEAR PORE COMPLEX PROTEIN NUP93 × 32 （Q8N1F7） NUCLEAR PORE COMPLEX PROTEIN NUP205 × 32 （Q92621） NUCLEAR PORE COMPLEX PROTEIN NUP54 × 32 （Q7Z3B4） NUCLEAR PORE COMPLEX PROTEIN NUP58 × 32 （Q9BVL2） Nuclear pore glycoprotein p62 × 32 （P37198） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 21.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5IJN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5A9Q Human nuclear pore complex Deposited 2015-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 304 PDB declaration: 304-meric
Chain A 1–1391（1391 aa）
Chain B 1–1391（1391 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
5IJO Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) Deposited 2016-03-02 Parsed fields agree Assembly 1 Protein heterocomplex Heteromer；Protein × 208 PDB declaration: 208-meric
Chain A 1–1391（1391 aa）
Chain B 1–1391（1391 aa）
Chain E 1–1391（1391 aa）
Chain K 1–1391（1391 aa）
Chain Q 1–1391（1391 aa）
Chain W 1–1391（1391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 21.40 Å
7EYE Cryo-EM (SPA) structure of Nup155 N-terminus (19-863) at 5.1 Angstrom resolution Deposited 2021-05-30 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 1–863（863 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was freshly made.
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging
Resolution 5.10 Å
7EYF Cryo-EM (SPA) structure of human Nup155 C-terminus (864-1337) at 5.3 Angstroms resolution Deposited 2021-05-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 864–1391（528 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was freshly made.
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging
Resolution 5.30 Å
7EYQ Cryo-EM (SPA) structure of human Nup155 Longer N-terminus (19-1069) at 5.4 Angstrom resolution Deposited 2021-05-31 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 1–1391（1391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was freshly made.
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging
Resolution 5.40 Å
7PER Model of the inner ring of the human nuclear pore complex Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric
Chain E 1–1391（1391 aa）
Chain K 1–1391（1391 aa）
Chain Q 1–1391（1391 aa）
Chain W 1–1391（1391 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
7R1Y cryoEM structure of human Nup155 (residues 19-981) Deposited 2022-02-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–1391（1390 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7R5J Human nuclear pore complex (dilated) Deposited 2022-02-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain D0 1–1391（1391 aa）
Chain D1 1–1391（1391 aa）
Chain D2 1–1391（1391 aa）
Chain D3 1–1391（1391 aa）
Chain D4 1–1391（1391 aa）
Chain D5 1–1391（1391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 50.00 Å
7R5K Human nuclear pore complex (constricted) Deposited 2022-02-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain D0 1–1391（1391 aa）
Chain D1 1–1391（1391 aa）
Chain D2 1–1391（1391 aa）
Chain D3 1–1391（1391 aa）
Chain D4 1–1391（1391 aa）
Chain D5 1–1391（1391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.00 Å

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

View Construct and Data Evidence
UniProt name NU155_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1391； UniProt 1–1391 Author chain B； PDBConstruct 1–1391； UniProt 1–1391 Author chain E； PDBConstruct 1–1391； UniProt 1–1391 Author chain K； PDBConstruct 1–1391； UniProt 1–1391 Author chain Q； PDBConstruct 1–1391； UniProt 1–1391 Author chain W； PDBConstruct 1–1391； UniProt 1–1391

NUCLEAR PORE COMPLEX PROTEIN NUP93

Homo sapiens

UniProt Q8N1F7

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 × 208 PDB declaration: 208-meric（208） Consistent with protein copy count Chain C； UniProt 1–819 Chain I； UniProt 1–819 Chain O； UniProt 1–819 Chain U； UniProt 1–819 Not recorded NUCLEAR PORE COMPLEX PROTEIN NUP155 × 48 （O75694） NUCLEAR PORE COMPLEX PROTEIN NUP205 × 32 （Q92621） NUCLEAR PORE COMPLEX PROTEIN NUP54 × 32 （Q7Z3B4） NUCLEAR PORE COMPLEX PROTEIN NUP58 × 32 （Q9BVL2） Nuclear pore glycoprotein p62 × 32 （P37198） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 21.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5IJN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IJO Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) Deposited 2016-03-02 Parsed fields agree Assembly 1 Protein heterocomplex Heteromer；Protein × 208 PDB declaration: 208-meric
Chain C 1–819（819 aa）
Chain I 1–819（819 aa）
Chain O 1–819（819 aa）
Chain U 1–819（819 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 21.40 Å
7MW0 Crystal structure of Homo sapiens NUP93 solenoid (residues 174-819) Deposited 2021-05-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 174–819（646 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.075 M TRIS pH 8.5, 19 % (w/v) PEG 20000
Resolution 2.00 Å R-free 0.254
7MW1 Crystal structure of the Homo sapiens NUP93-NUP53 complex (NUP93 residues 174-819; NUP53 residues 84-150) Deposited 2021-05-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 174–819（646 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.075 M TRIS pH 8.5, 17% (w/v) PEG 20000
Resolution 3.40 Å R-free 0.276
7MW1 Crystal structure of the Homo sapiens NUP93-NUP53 complex (NUP93 residues 174-819; NUP53 residues 84-150) Deposited 2021-05-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 174–819（646 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.075 M TRIS pH 8.5, 17% (w/v) PEG 20000
Resolution 3.40 Å R-free 0.276
7PER Model of the inner ring of the human nuclear pore complex Deposited 2021-08-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric
Chain C 1–819（819 aa）
Chain I 1–819（819 aa）
Chain O 1–819（819 aa）
Chain U 1–819（819 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 mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain A0 1–819（819 aa）
Chain A1 1–819（819 aa）
Chain A2 1–819（819 aa）
Chain A3 1–819（819 aa）
Chain A4 1–819（819 aa）
Chain A5 1–819（819 aa）
Chain A6 1–819（819 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain A0 1–819（819 aa）
Chain A1 1–819（819 aa）
Chain A2 1–819（819 aa）
Chain A3 1–819（819 aa）
Chain A4 1–819（819 aa）
Chain A5 1–819（819 aa）
Chain A6 1–819（819 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

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

View Construct and Data Evidence
UniProt name NUP93_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–819； UniProt 1–819 Author chain I； PDBConstruct 1–819； UniProt 1–819 Author chain O； PDBConstruct 1–819； UniProt 1–819 Author chain U； PDBConstruct 1–819； UniProt 1–819

NUCLEAR PORE COMPLEX PROTEIN NUP205

Homo sapiens

UniProt Q92621

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 × 208 PDB declaration: 208-meric（208） Consistent with protein copy count Chain D； UniProt 1–2012 Chain J； UniProt 1–2012 Chain P； UniProt 1–2012 Chain V； UniProt 1–2012 Not recorded NUCLEAR PORE COMPLEX PROTEIN NUP155 × 48 （O75694） NUCLEAR PORE COMPLEX PROTEIN NUP93 × 32 （Q8N1F7） NUCLEAR PORE COMPLEX PROTEIN NUP54 × 32 （Q7Z3B4） NUCLEAR PORE COMPLEX PROTEIN NUP58 × 32 （Q9BVL2） Nuclear pore glycoprotein p62 × 32 （P37198） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 21.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5IJN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IJO Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) Deposited 2016-03-02 Different construct Different mutation/modification Assembly 1 Protein heterocomplex Heteromer；Protein × 208 PDB declaration: 208-meric
Chain D 1–2012（2012 aa）
Chain P 1–2012（2012 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 21.40 Å
7PER Model of the inner ring of the human nuclear pore complex Deposited 2021-08-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric
Chain D 1–2012（2012 aa）
Chain J 1–2012（2012 aa）
Chain P 1–2012（2012 aa）
Chain V 1–2012（2012 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 mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain C0 1–2012（2012 aa）
Chain C1 1–2012（2012 aa）
Chain C2 1–2012（2012 aa）
Chain C3 1–2012（2012 aa）
Chain C4 1–2012（2012 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain C0 1–2012（2012 aa）
Chain C1 1–2012（2012 aa）
Chain C2 1–2012（2012 aa）
Chain C3 1–2012（2012 aa）
Chain C4 1–2012（2012 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

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

View Construct and Data Evidence
UniProt name NU205_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–2012； UniProt 1–2012 Author chain J； PDBConstruct 1–2012； UniProt 1–2012 Author chain P； PDBConstruct 1–2012； UniProt 1–2012 Author chain V； PDBConstruct 1–2012； UniProt 1–2012

NUCLEAR PORE COMPLEX PROTEIN NUP54

Homo sapiens

UniProt Q7Z3B4

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 × 208 PDB declaration: 208-meric（208） Consistent with protein copy count Chain F； UniProt 1–507 Chain L； UniProt 1–507 Chain R； UniProt 1–507 Chain X； UniProt 1–507 Not recorded NUCLEAR PORE COMPLEX PROTEIN NUP155 × 48 （O75694） NUCLEAR PORE COMPLEX PROTEIN NUP93 × 32 （Q8N1F7） NUCLEAR PORE COMPLEX PROTEIN NUP205 × 32 （Q92621） NUCLEAR PORE COMPLEX PROTEIN NUP58 × 32 （Q9BVL2） Nuclear pore glycoprotein p62 × 32 （P37198） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 21.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5IJN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4JNU Crystal structure of the human Nup57CCS3* coiled-coil segment, space group P21 Deposited 2013-03-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 453–491（39 aa） Fragment：UNP residues 453-491
Chain B 453–491（39 aa） Fragment：UNP residues 453-491
Chain C 453–491（39 aa） Fragment：UNP residues 453-491
Chain D 453–491（39 aa） Fragment：UNP residues 453-491
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；294 K；0.1 M sodium acetate, pH 5.3, 1.9 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.45 Å R-free 0.218
4JNV Crystal structure of the human Nup57CCS3* coiled-coil segment, space group C2 Deposited 2013-03-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 453–491（39 aa） Fragment：UNP residues 453-491
Chain B 453–491（39 aa） Fragment：UNP residues 453-491
Chain C 453–491（39 aa） Fragment：UNP residues 453-491
Chain D 453–491（39 aa） Fragment：UNP residues 453-491
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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 5.3；294 K；0.1 M sodium acetate, pH 5.3, 1.9 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.85 Å R-free 0.277
4JO7 Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex with 2:2 stoichiometry Deposited 2013-03-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 453–491（39 aa） Fragment：UNP residues 453-491
Chain D 453–491（39 aa） Fragment：UNP residues 453-491
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M MES, pH 6.5, 6.7% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Resolution 1.75 Å R-free 0.214
4JO7 Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex with 2:2 stoichiometry Deposited 2013-03-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 453–491（39 aa） Fragment：UNP residues 453-491
Chain H 453–491（39 aa） Fragment：UNP residues 453-491
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M MES, pH 6.5, 6.7% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Resolution 1.75 Å R-free 0.214
4JO9 Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex 1:2 stoichiometry Deposited 2013-03-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 453–491（39 aa） Fragment：UNP residues 453-491
Chain C 453–491（39 aa） Fragment：UNP residues 453-491
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 3.8；294 K；0.1 M sodium citrate, pH 3.8, 0.07 M calcium chloride, VAPOR DIFFUSION, temperature 294.0K
Resolution 2.50 Å R-free 0.294
5IJO Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) Deposited 2016-03-02 Parsed fields agree Assembly 1 Protein heterocomplex Heteromer；Protein × 208 PDB declaration: 208-meric
Chain F 1–507（507 aa）
Chain L 1–507（507 aa）
Chain R 1–507（507 aa）
Chain X 1–507（507 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 21.40 Å
7PER Model of the inner ring of the human nuclear pore complex Deposited 2021-08-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric
Chain F 1–507（507 aa）
Chain L 1–507（507 aa）
Chain R 1–507（507 aa）
Chain X 1–507（507 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 oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain H0 1–507（507 aa）
Chain H1 1–507（507 aa）
Chain H2 1–507（507 aa）
Chain H3 1–507（507 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain H0 1–507（507 aa）
Chain H1 1–507（507 aa）
Chain H2 1–507（507 aa）
Chain H3 1–507（507 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

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

View Construct and Data Evidence
UniProt name NUP54_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain F； PDBConstruct 1–507； UniProt 1–507 Author chain L； PDBConstruct 1–507； UniProt 1–507 Author chain R； PDBConstruct 1–507； UniProt 1–507 Author chain X； PDBConstruct 1–507； UniProt 1–507

NUCLEAR PORE COMPLEX PROTEIN NUP58

Homo sapiens

UniProt Q9BVL2

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 × 208 PDB declaration: 208-meric（208） Consistent with protein copy count Chain G； UniProt 1–599 Chain M； UniProt 1–599 Chain S； UniProt 1–599 Chain Y； UniProt 1–599 Not recorded NUCLEAR PORE COMPLEX PROTEIN NUP155 × 48 （O75694） NUCLEAR PORE COMPLEX PROTEIN NUP93 × 32 （Q8N1F7） NUCLEAR PORE COMPLEX PROTEIN NUP205 × 32 （Q92621） NUCLEAR PORE COMPLEX PROTEIN NUP54 × 32 （Q7Z3B4） Nuclear pore glycoprotein p62 × 32 （P37198） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 21.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5IJN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4JO7 Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex with 2:2 stoichiometry Deposited 2013-03-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 341–428（88 aa） Fragment：UNP residues 341-428
Chain C 341–428（88 aa） Fragment：UNP residues 341-428
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M MES, pH 6.5, 6.7% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Resolution 1.75 Å R-free 0.214
4JO7 Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex with 2:2 stoichiometry Deposited 2013-03-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 341–428（88 aa） Fragment：UNP residues 341-428
Chain G 341–428（88 aa） Fragment：UNP residues 341-428
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M MES, pH 6.5, 6.7% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Resolution 1.75 Å R-free 0.214
4JO9 Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex 1:2 stoichiometry Deposited 2013-03-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 341–426（86 aa） Fragment：UNP residues 341-426
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 3.8；294 K；0.1 M sodium citrate, pH 3.8, 0.07 M calcium chloride, VAPOR DIFFUSION, temperature 294.0K
Resolution 2.50 Å R-free 0.294
4JQ5 Crystal structure of the human Nup49CCS2+3* coiled-coil segment Deposited 2013-03-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 341–425（85 aa） Fragment：UNP residues 341-425
Chain B 341–425（85 aa） Fragment：UNP residues 341-425
Chain C 341–425（85 aa） Fragment：UNP residues 341-425
Chain D 341–425（85 aa） Fragment：UNP residues 341-425
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；10% glycerol, 28% dioxane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Resolution 2.19 Å R-free 0.293
4JQ5 Crystal structure of the human Nup49CCS2+3* coiled-coil segment Deposited 2013-03-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 341–425（85 aa） Fragment：UNP residues 341-425
Chain F 341–425（85 aa） Fragment：UNP residues 341-425
Chain G 341–425（85 aa） Fragment：UNP residues 341-425
Chain H 341–425（85 aa） Fragment：UNP residues 341-425
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；10% glycerol, 28% dioxane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Resolution 2.19 Å R-free 0.293
4JQ5 Crystal structure of the human Nup49CCS2+3* coiled-coil segment Deposited 2013-03-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain I 341–425（85 aa） Fragment：UNP residues 341-425
Chain J 341–425（85 aa） Fragment：UNP residues 341-425
Chain K 341–425（85 aa） Fragment：UNP residues 341-425
Chain L 341–425（85 aa） Fragment：UNP residues 341-425
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；10% glycerol, 28% dioxane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Resolution 2.19 Å R-free 0.293
5IJO Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) Deposited 2016-03-02 Parsed fields agree Assembly 1 Protein heterocomplex Heteromer；Protein × 208 PDB declaration: 208-meric
Chain G 1–599（599 aa）
Chain M 1–599（599 aa）
Chain S 1–599（599 aa）
Chain Y 1–599（599 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 21.40 Å
7PER Model of the inner ring of the human nuclear pore complex Deposited 2021-08-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric
Chain G 1–599（599 aa）
Chain M 1–599（599 aa）
Chain S 1–599（599 aa）
Chain Y 1–599（599 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 oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain I0 1–599（599 aa）
Chain I1 1–599（599 aa）
Chain I2 1–599（599 aa）
Chain I3 1–599（599 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain I0 1–599（599 aa）
Chain I1 1–599（599 aa）
Chain I2 1–599（599 aa）
Chain I3 1–599（599 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

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

View Construct and Data Evidence
UniProt name NUP58_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain G； PDBConstruct 1–599； UniProt 1–599 Author chain M； PDBConstruct 1–599； UniProt 1–599 Author chain S； PDBConstruct 1–599； UniProt 1–599 Author chain Y； PDBConstruct 1–599； UniProt 1–599

Nuclear pore glycoprotein p62

Homo sapiens

UniProt P37198

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 × 208 PDB declaration: 208-meric（208） Consistent with protein copy count Chain H； UniProt 1–522 Chain N； UniProt 1–522 Chain T； UniProt 1–522 Chain Z； UniProt 1–522 Not recorded NUCLEAR PORE COMPLEX PROTEIN NUP155 × 48 （O75694） NUCLEAR PORE COMPLEX PROTEIN NUP93 × 32 （Q8N1F7） NUCLEAR PORE COMPLEX PROTEIN NUP205 × 32 （Q92621） NUCLEAR PORE COMPLEX PROTEIN NUP54 × 32 （Q7Z3B4） NUCLEAR PORE COMPLEX PROTEIN NUP58 × 32 （Q9BVL2） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 21.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5IJN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IJO Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) Deposited 2016-03-02 Parsed fields agree Assembly 1 Protein heterocomplex Heteromer；Protein × 208 PDB declaration: 208-meric
Chain H 1–522（522 aa）
Chain N 1–522（522 aa）
Chain T 1–522（522 aa）
Chain Z 1–522（522 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 21.40 Å
7PER Model of the inner ring of the human nuclear pore complex Deposited 2021-08-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric
Chain H 1–522（522 aa）
Chain N 1–522（522 aa）
Chain T 1–522（522 aa）
Chain Z 1–522（522 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 mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain J0 1–522（522 aa）
Chain J1 1–522（522 aa）
Chain J2 1–522（522 aa）
Chain J3 1–522（522 aa）
Chain J4 1–522（522 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain J0 1–522（522 aa）
Chain J1 1–522（522 aa）
Chain J2 1–522（522 aa）
Chain J3 1–522（522 aa）
Chain J4 1–522（522 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

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

View Construct and Data Evidence
UniProt name NUP62_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain H； PDBConstruct 1–522； UniProt 1–522 Author chain N； PDBConstruct 1–522； UniProt 1–522 Author chain T； PDBConstruct 1–522； UniProt 1–522 Author chain Z； PDBConstruct 1–522； UniProt 1–522

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 5ijn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ijn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ijn
Deposition date deposition_date2016-03-02
Structure title titleComposite structure of the inner ring of the human nuclear pore complex (32 copies of Nup205)
Keywords keywordsNuclear pore complex, Nucleocytoplasmic transport, Transport protein; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier— Å
Radius of gyration Rg (electron density) rg_electron108.00 Å
Forward intensity I(0) i01394240000000.00
Molecular weight molecular_weight8318000.0 kDa
Excluded volume excluded_volume9592000 ų
Envelope volume envelope_volume4773200 ų
Hydration-shell volume shell_volume374190 ų
Envelope diameter envelope_diameter399.0 Å
Shell Rg shell_rg103.70 Å
Envelope Rg envelope_rg101.20 Å
Shape Rg shape_rg108.00 Å
Total Rg total_rg108.00 Å
Total atoms total_atoms594304
Residues n_residues119904
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 dmax283.3 Å
Rg (real space) rg_real104.60 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real1.3270e+12
I(0) uncertainty (real space) i0_real_error2.4220e+10
Rg (reciprocal space) rg_reciprocal110.50 Å
I(0) (reciprocal space) i0_reciprocal1404000000000.0000
Solution quality estimate total_estimate0.9004
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary121.4 Å
Skewness Skewness skewness0.104
Kurtosis Kurtosis kurtosis-0.502
Angular range angular_range— – 0.0700 Å−1
Current regularization parameter α current_alpha1.1860
Highest regularization parameter α highest_alpha3842000000.0000
Real-space data points n_real_points15
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.002; Oscil: 0.998; Stabil: 0.965; Sysdev: 1.000; Positv: 1.000; Valcen: 0.822; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)