SAXSdb — 3hxr

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

Nucleoporin NUP120

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 1–757	Fragment：UNP residues 1-757 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 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

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 3HXR	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
3H7N Structure of Nup120 Deposited 2009-04-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–729（729 aa）	Not recorded	No recorded non-water small molecule	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
3H7N Structure of Nup120 Deposited 2009-04-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–729（729 aa）	Not recorded	No recorded non-water small molecule	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
3H7N Structure of Nup120 Deposited 2009-04-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–729（729 aa）	Not recorded	No recorded non-water small molecule	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
3H7N Structure of Nup120 Deposited 2009-04-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–729（729 aa）	Not recorded	No recorded non-water small molecule	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
4XMM Structure of the yeast coat nucleoporin complex, space group C2 Deposited 2015-01-14	Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 20 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 5–761； UniProt 1–757

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	3hxr
Deposition date deposition_date	2009-06-21
Structure title title	Nucleoporin Nup120 from S.cerevisiae (aa 1-757)
Keywords keywords	;structural protein, Coiled coil, Membrane, mRNA transport, Nuclear pore complex, Nucleus, Phosphoprotein, Protein transport, Translocation, Transport ;; STRUCTURAL 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	29.31 Å
Radius of gyration Rg (electron density) rg_electron	28.67 Å
Forward intensity I(0) i0	86658800.00
Molecular weight molecular_weight	75572.0 kDa
Excluded volume excluded_volume	95212 Å³
Envelope volume envelope_volume	119310 Å³
Hydration-shell volume shell_volume	35078 Å³
Envelope diameter envelope_diameter	105.9 Å
Shell Rg shell_rg	35.65 Å
Envelope Rg envelope_rg	28.87 Å
Shape Rg shape_rg	28.68 Å
Total Rg total_rg	29.33 Å
Total atoms total_atoms	5313
Residues n_residues	651
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	98.1 Å
Rg (real space) rg_real	29.34 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	8.6660e+07
I(0) uncertainty (real space) i0_real_error	1.4390e+06
Rg (reciprocal space) rg_reciprocal	29.33 Å
I(0) (reciprocal space) i0_reciprocal	86660000.0000
Solution quality estimate total_estimate	0.8049
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.7 Å
Skewness Skewness skewness	0.422
Kurtosis Kurtosis kurtosis	-0.232
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27580000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; 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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Unit-cell length a length_a	114.600 Å
Unit-cell length b length_b	153.690 Å
Unit-cell length c length_c	52.980 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	48.090 Å
R factor r_factor	0.2470
R_work r_work	0.2440
R_free r_free	0.2990

Description description	Nucleoporin NUP120
Molecular weight formula_weight	88065.8 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	5313

Nucleoporin Nup120 from S.cerevisiae (aa 1-757)

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

Nucleoporin NUP120

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

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/hx/3hxr/3hxr.fit
pddf	/app/data/pr_computation/hx/3hxr/3hxr.pr.out
profile	/app/data/saxs_computation/hx/3hxr/3hxr.dat