SAXSdb — 3i5p

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin NUP170

Saccharomyces cerevisiae

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 980–1502	Fragment：HELICAL DOMAIN (UNP residues 980-1502)	No other associated polymer	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

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 3I5P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3I5Q Nup170(aa1253-1502) at 2.2 A, 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 B 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)	Not recorded	No recorded non-water small molecule	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
3I5Q Nup170(aa1253-1502) at 2.2 A, S.cerevisiae Deposited 2009-07-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)	Not recorded	No recorded non-water small molecule	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
3I5Q Nup170(aa1253-1502) at 2.2 A, S.cerevisiae Deposited 2009-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502) Chain B 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)	Not recorded	No recorded non-water small molecule	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
3I5Q Nup170(aa1253-1502) at 2.2 A, S.cerevisiae Deposited 2009-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502) Chain B 1253–1502（250 aa） Fragment：C-terminal fragment (UNP residues 1253-1502)	Not recorded	No recorded non-water small molecule	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
7N85 Inner ring spoke 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 × 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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 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 mutation/modification 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 mutation/modification 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 13 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 3–525； UniProt 980–1502

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3i5p
Deposition date deposition_date	2009-07-06
Structure title title	Nup170(aa979-1502), S.cerevisiae
Keywords keywords	;HELICAL STACK, Membrane, mRNA transport, Nuclear pore complex, Nucleus, Phosphoprotein, Protein transport, Translocation, Transmembrane, Transport ;; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.22 Å
Radius of gyration Rg (electron density) rg_electron	36.15 Å
Forward intensity I(0) i0	37154900.00
Molecular weight molecular_weight	50217.0 kDa
Excluded volume excluded_volume	63520 Å³
Envelope volume envelope_volume	87420 Å³
Hydration-shell volume shell_volume	22966 Å³
Envelope diameter envelope_diameter	125.0 Å
Shell Rg shell_rg	36.71 Å
Envelope Rg envelope_rg	36.26 Å
Shape Rg shape_rg	36.16 Å
Total Rg total_rg	36.16 Å
Total atoms total_atoms	3551
Residues n_residues	449
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	116.9 Å
Rg (real space) rg_real	36.82 Å
Rg uncertainty (real space) rg_real_error	1.30 Å
I(0) (real space) i0_real	3.7150e+07
I(0) uncertainty (real space) i0_real_error	6.7880e+05
Rg (reciprocal space) rg_reciprocal	36.45 Å
I(0) (reciprocal space) i0_reciprocal	37140000.0000
Solution quality estimate total_estimate	0.7167
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.533
Kurtosis Kurtosis kurtosis	-0.636
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2896000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.631; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.310; Smooth: 0.111

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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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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3i5pA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	450 — Nucleoporin, helical domain, N-terminal subdomain

Domain ID domain_id	3i5pA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	440 — Nucleoporin, helical domain, central subdomain

Domain ID domain_id	3i5pA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1880 — Nucleoporin, helical C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	121.370 Å
Unit-cell length b length_b	121.370 Å
Unit-cell length c length_c	256.729 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	28.966 Å
R factor r_factor	0.3074
R_work r_work	0.3067
R_free r_free	0.3241

Description description	Nucleoporin NUP170
Molecular weight formula_weight	61120.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3551

Nup170(aa979-1502), S.cerevisiae

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin NUP170

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/i5/3i5p/3i5p.fit
pddf	/app/data/pr_computation/i5/3i5p/3i5p.pr.out
profile	/app/data/saxs_computation/i5/3i5p/3i5p.dat