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3i5q

Nup170(aa1253-1502) at 2.2 A, S.cerevisiae

Method: X-RAY DIFFRACTION Dmax: 78.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin NUP170

Saccharomyces cerevisiae

UniProt P38181

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 B； UniProt 1253–1502 Fragment：C-terminal fragment (UNP residues 1253-1502) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M LITHIUM SULFATE, 0.1M TRIS-HCL, 50 mM NACL, 22% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.20 Å R-free 0.272
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1253–1502 Fragment：C-terminal fragment (UNP residues 1253-1502) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M LITHIUM SULFATE, 0.1M TRIS-HCL, 50 mM NACL, 22% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.20 Å R-free 0.272
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1253–1502 Chain B； UniProt 1253–1502 Fragment：C-terminal fragment (UNP residues 1253-1502) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M LITHIUM SULFATE, 0.1M TRIS-HCL, 50 mM NACL, 22% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.20 Å R-free 0.272
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1253–1502 Chain B； UniProt 1253–1502 Fragment：C-terminal fragment (UNP residues 1253-1502) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M LITHIUM SULFATE, 0.1M TRIS-HCL, 50 mM NACL, 22% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.20 Å R-free 0.272

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 3I5Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3I5P Nup170(aa979-1502), S.cerevisiae Deposited 2009-07-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 980–1502（523 aa） Fragment：HELICAL DOMAIN (UNP residues 980-1502)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；289 K；0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, 8% PEG 3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.20 Å R-free 0.324
7N85 Inner ring spoke 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 × 240 PDB declaration: 240-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–1502（1502 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain D 1–1502（1502 aa）
Chain P 1–1502（1502 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric
Chain 0 1–1502（1502 aa）
Chain Y 1–1502（1502 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

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

View Construct and Data Evidence
UniProt name NU170_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–252； UniProt 1253–1502 Author chain B； PDBConstruct 3–252； UniProt 1253–1502

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 3i5q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3i5q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3i5q
Deposition date deposition_date2009-07-06
Structure title titleNup170(aa1253-1502) at 2.2 A, S.cerevisiae
Keywords keywords;HELICAL STACK, Membrane, mRNA transport, Nuclear pore complex, Nucleus, Phosphoprotein, Protein transport, Translocation, Transmembrane, Transport ;; 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_guinier26.32 Å
Radius of gyration Rg (electron density) rg_electron24.86 Å
Forward intensity I(0) i049223000.00
Molecular weight molecular_weight57356.0 kDa
Excluded volume excluded_volume72930 ų
Envelope volume envelope_volume91295 ų
Hydration-shell volume shell_volume29989 ų
Envelope diameter envelope_diameter78.6 Å
Shell Rg shell_rg32.77 Å
Envelope Rg envelope_rg24.53 Å
Shape Rg shape_rg24.85 Å
Total Rg total_rg25.84 Å
Total atoms total_atoms4052
Residues n_residues496
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 dmax78.9 Å
Rg (real space) rg_real26.15 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real4.9220e+07
I(0) uncertainty (real space) i0_real_error7.2810e+05
Rg (reciprocal space) rg_reciprocal26.20 Å
I(0) (reciprocal space) i0_reciprocal49220000.0000
Solution quality estimate total_estimate0.9126
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.5 Å
Skewness Skewness skewness0.064
Kurtosis Kurtosis kurtosis-0.567
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9610000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.959; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.995
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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) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3i5qA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily1050 —
Domain ID domain_id3i5qA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology167 — Regulator of G-protein Signalling 4; domain 2
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3i5qB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily1050 —
Domain ID domain_id3i5qB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology167 — Regulator of G-protein Signalling 4; domain 2
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)