SAXSdb — 1xip

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

Nucleoporin NUP159

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 2–387	Fragment：N-terminal domain Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；292 K；PEG3350, ammonium acetate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.50 Å R-free 0.249

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 1XIP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3PBP Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex Deposited 2010-10-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1425–1460（36 aa） Fragment：Tail, UNP residues 1425-1460	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, SITTING DROP；pH 6.6；298 K；PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.272
3PBP Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex Deposited 2010-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1425–1460（36 aa） Fragment：Tail, UNP residues 1425-1460	Non-standard monomer：Yes (specific site not provided by mmCIF)	PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；298 K；PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.272
3PBP Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex Deposited 2010-10-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1425–1460（36 aa） Fragment：Tail, UNP residues 1425-1460	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, SITTING DROP；pH 6.6；298 K；PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.272
3PBP Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex Deposited 2010-10-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1425–1460（36 aa） Fragment：Tail, UNP residues 1425-1460	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, SITTING DROP；pH 6.6；298 K；PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.272
3RRM S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp Deposited 2011-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–387（386 aa） Fragment：unp residues 2-387	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；20% PEG 3350, 200 mM KOAc, 20 mM sarcosine, 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 0.5 mM IP6, 10 mM MgCl2, 1 mM ADP, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.261
3TKN Structure of the Nup82-Nup159-Nup98 heterotrimer Deposited 2011-08-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1425–1460（36 aa） Fragment：UNP residues 1425-1460	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；18.5% PEG3350, 100 mM potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.40 Å R-free 0.285
3TKN Structure of the Nup82-Nup159-Nup98 heterotrimer Deposited 2011-08-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1425–1460（36 aa） Fragment：UNP residues 1425-1460	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；18.5% PEG3350, 100 mM potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.40 Å R-free 0.285
3TKN Structure of the Nup82-Nup159-Nup98 heterotrimer Deposited 2011-08-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1425–1460（36 aa） Fragment：UNP residues 1425-1460	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；18.5% PEG3350, 100 mM potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.40 Å R-free 0.285
4DS1 The Structure of a Yeast Dyn2-Nup159 Complex and the Molecular Basis for the Dynein Light Chain - Nuclear Pore Interaction Deposited 2012-02-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1116–1126（11 aa） Fragment：UNP residues 1116-1126 Chain D 1116–1126（11 aa） Fragment：UNP residues 1116-1126	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.3 M Ammonium acetate, 5% methyl pentanediol (v/v), 35% PEG 4000 (w/v), pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.187
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 w 1–1460（1460 aa） Chain x 1–1460（1460 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 w 1–1460（1460 aa） Chain x 1–1460（1460 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 w 1–1460（1460 aa） Chain x 1–1460（1460 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

5 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NU159_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–388； UniProt 2–387

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	1xip
Deposition date deposition_date	2004-09-21
Structure title title	Crystal Structure of the N-terminal Domain of Nup159
Keywords keywords	beta-propeller, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	21.39 Å
Radius of gyration Rg (electron density) rg_electron	19.96 Å
Forward intensity I(0) i0	27508700.00
Molecular weight molecular_weight	40964.0 kDa
Excluded volume excluded_volume	51507 Å³
Envelope volume envelope_volume	60813 Å³
Hydration-shell volume shell_volume	24418 Å³
Envelope diameter envelope_diameter	66.9 Å
Shell Rg shell_rg	27.43 Å
Envelope Rg envelope_rg	20.21 Å
Shape Rg shape_rg	19.97 Å
Total Rg total_rg	20.90 Å
Total atoms total_atoms	2883
Residues n_residues	364
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	64.7 Å
Rg (real space) rg_real	21.21 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	2.7510e+07
I(0) uncertainty (real space) i0_real_error	2.9600e+05
Rg (reciprocal space) rg_reciprocal	21.25 Å
I(0) (reciprocal space) i0_reciprocal	27510000.0000
Solution quality estimate total_estimate	0.9039
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.084
Kurtosis Kurtosis kurtosis	-0.487
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8131000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.998

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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1xipa1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.14 — Nucleoporin domain
Family Family family	b.69.14.1 — Nucleoporin domain

Domain ID domain_id	d1xipa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1xipA00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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8. Citations (1)

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Unit-cell length a length_a	60.359 Å
Unit-cell length b length_b	71.516 Å
Unit-cell length c length_c	90.728 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2058
R_work r_work	0.2035
R_free r_free	0.2489

Description description	Nucleoporin NUP159
Molecular weight formula_weight	43177.9 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	2981

Crystal Structure of the N-terminal Domain of Nup159

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

Nucleoporin NUP159

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 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	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

fit	/app/data/saxs_computation/xi/1xip/1xip.fit
pddf	/app/data/pr_computation/xi/1xip/1xip.pr.out
profile	/app/data/saxs_computation/xi/1xip/1xip.dat