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3h7n

Structure of Nup120

Method: X-RAY DIFFRACTION Dmax: 204.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin NUP120

Saccharomyces cerevisiae

UniProt P35729

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–729 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Sodium citrate (tribasic dihydrate), Potassium thiocynate, PEG 2000 MME, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 3.00 Å R-free 0.274
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–729 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Sodium citrate (tribasic dihydrate), Potassium thiocynate, PEG 2000 MME, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 3.00 Å R-free 0.274
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–729 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Sodium citrate (tribasic dihydrate), Potassium thiocynate, PEG 2000 MME, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 3.00 Å R-free 0.274
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 1–729 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Sodium citrate (tribasic dihydrate), Potassium thiocynate, PEG 2000 MME, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 3.00 Å R-free 0.274

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 3H7N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3F7F Structure of Nup120 Deposited 2008-11-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–729（729 aa） Fragment：UNP residues 1-729
Mutation：S207C HG MERCURY (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Succinic acid, PEG 3350, Sodium bromide, Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.254
3F7F Structure of Nup120 Deposited 2008-11-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–729（729 aa） Fragment：UNP residues 1-729
Mutation：S207C HG MERCURY (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Succinic acid, PEG 3350, Sodium bromide, Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.254
3F7F Structure of Nup120 Deposited 2008-11-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–729（729 aa） Fragment：UNP residues 1-729
Mutation：S207C HG MERCURY (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Succinic acid, PEG 3350, Sodium bromide, Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.254
3F7F Structure of Nup120 Deposited 2008-11-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–729（729 aa） Fragment：UNP residues 1-729
Mutation：S207C HG MERCURY (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Succinic acid, PEG 3350, Sodium bromide, Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.254
3F7F Structure of Nup120 Deposited 2008-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–729（729 aa） Fragment：UNP residues 1-729
Chain B 1–729（729 aa） Fragment：UNP residues 1-729
Mutation：S207C Mutation：S207C HG MERCURY (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Succinic acid, PEG 3350, Sodium bromide, Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.254
3F7F Structure of Nup120 Deposited 2008-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–729（729 aa） Fragment：UNP residues 1-729
Chain D 1–729（729 aa） Fragment：UNP residues 1-729
Mutation：S207C Mutation：S207C HG MERCURY (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Succinic acid, PEG 3350, Sodium bromide, Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.254
3HXR Nucleoporin Nup120 from S.cerevisiae (aa 1-757) Deposited 2009-06-21 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–757（757 aa） Fragment：UNP residues 1-757
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；291 K；15% PEG3350, 0.2M KSCN, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.00 Å R-free 0.299
4XMM Structure of the yeast coat nucleoporin complex, space group C2 Deposited 2015-01-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 2–1037（1036 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 E 1–1037（1037 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 7.60 Å R-free 0.347
6X06 Nup120 (aa1-757) from S. cerevisiae bound by VHH-SAN11 Deposited 2020-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–757（757 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；19% PEG 8,000, 0.1M magnesium chloride, 0.1M Tris/HCl pH 8.5
Resolution 4.27 Å R-free 0.359
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 a 1–1037（1037 aa）
Chain l 1–1037（1037 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 a 1–1037（1037 aa）
Chain l 1–1037（1037 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 a 1–1037（1037 aa）
Chain l 1–1037（1037 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 a 1–1037（1037 aa）
Chain h 1–1037（1037 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 a 1–1037（1037 aa）
Chain h 1–1037（1037 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 a 1–1037（1037 aa）
Chain h 1–1037（1037 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 a 1–1037（1037 aa）
Chain l 1–1037（1037 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 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NU120_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–729； UniProt 1–729 Author chain B； PDBConstruct 1–729； UniProt 1–729 Author chain C； PDBConstruct 1–729； UniProt 1–729 Author chain D； PDBConstruct 1–729； UniProt 1–729

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 3h7n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3h7n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3h7n
Deposition date deposition_date2009-04-27
Structure title titleStructure of Nup120
Keywords keywords;Nucleoporin, Nuclear Pore Complex, Macromolecular Assembly, Membrane Coat, Nucleocytoplasmic Transport, beta-propeller, alpha-helical solenoid domain, Coiled coil, Membrane, mRNA transport, Nucleus, Phosphoprotein, Protein transport, Translocation, Transport, STRUCTURAL PROTEIN ;; STRUCTURAL PROTEIN
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_guinier58.91 Å
Radius of gyration Rg (electron density) rg_electron59.13 Å
Forward intensity I(0) i01372880000.00
Molecular weight molecular_weight325230.0 kDa
Excluded volume excluded_volume412150 ų
Envelope volume envelope_volume607960 ų
Hydration-shell volume shell_volume87886 ų
Envelope diameter envelope_diameter205.4 Å
Shell Rg shell_rg58.57 Å
Envelope Rg envelope_rg57.83 Å
Shape Rg shape_rg59.12 Å
Total Rg total_rg59.14 Å
Total atoms total_atoms22992
Residues n_residues2824
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 dmax204.8 Å
Rg (real space) rg_real59.12 Å
Rg uncertainty (real space) rg_real_error2.12 Å
I(0) (real space) i0_real1.3730e+09
I(0) uncertainty (real space) i0_real_error2.9760e+07
Rg (reciprocal space) rg_reciprocal58.70 Å
I(0) (reciprocal space) i0_reciprocal1372000000.0000
Solution quality estimate total_estimate0.8080
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary68.3 Å
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.457
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha100600000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)