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4ifq

Crystal structure of Saccharomyces cerevisiae NUP192, residues 2 to 960 [ScNup192(2-960)]

Method: X-RAY DIFFRACTION Dmax: 107.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin NUP192

Saccharomyces cerevisiae

UniProt P47054

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 2–960 Fragment：UNP residues 2-960 Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 7 IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；Protein (20 mM Hepes, pH 8.0, 500 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (10% PEG3350, 100mM pottasium iodide); Cryoprotection (30% PEG400 and 25% saturated ammonium sulfate), Vapor Diffusion, Sitting Drop, temperature 298K Resolution 3.25 Å R-free 0.243
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–960 Fragment：UNP residues 2-960 Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 14 IOD IODIDE ION × 14 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；Protein (20 mM Hepes, pH 8.0, 500 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (10% PEG3350, 100mM pottasium iodide); Cryoprotection (30% PEG400 and 25% saturated ammonium sulfate), Vapor Diffusion, Sitting Drop, temperature 298K Resolution 3.25 Å R-free 0.243

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 4IFQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 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
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–1683（1683 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
7WOT Cryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain F 1–1683（1683 aa）
Chain R 1–1683（1683 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain M 1–1683（1683 aa）
Chain O 1–1683（1683 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 6.60 Å

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

View Construct and Data Evidence
UniProt name NU192_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–962； UniProt 2–960

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 4ifq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ifq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ifq
Deposition date deposition_date2012-12-14
Structure title titleCrystal structure of Saccharomyces cerevisiae NUP192, residues 2 to 960 [ScNup192(2-960)]
Keywords keywords;Structural genomics, NYSGRC, PSI-Biology, New York Structural Genomics Research Consortium, alpha solenoid-like, Nuclear Pore Complex component, NPC, Nup192, Nup188, Nucleoporin, PROTEIN TRANSPORT, Nucleocytoplasmic Transport: a Target for Cellular Control, NPCXstals ;; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.09 Å
Radius of gyration Rg (electron density) rg_electron33.33 Å
Forward intensity I(0) i0149179000.00
Molecular weight molecular_weight99782.0 kDa
Excluded volume excluded_volume125110 ų
Envelope volume envelope_volume158990 ų
Hydration-shell volume shell_volume39485 ų
Envelope diameter envelope_diameter107.8 Å
Shell Rg shell_rg40.32 Å
Envelope Rg envelope_rg32.89 Å
Shape Rg shape_rg33.33 Å
Total Rg total_rg33.85 Å
Total atoms total_atoms6965
Residues n_residues844
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 dmax107.3 Å
Rg (real space) rg_real34.04 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real1.4920e+08
I(0) uncertainty (real space) i0_real_error2.3620e+06
Rg (reciprocal space) rg_reciprocal34.08 Å
I(0) (reciprocal space) i0_reciprocal149200000.0000
Solution quality estimate total_estimate0.9045
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.0 Å
Skewness Skewness skewness0.193
Kurtosis Kurtosis kurtosis-0.691
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35120000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.904
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)