SAXSdb — 7mw0

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

Nuclear pore complex protein Nup93

Homo sapiens

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 174–819	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.075 M TRIS pH 8.5, 19 % (w/v) PEG 20000	Resolution 2.00 Å R-free 0.254

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 7MW0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5IJN Composite structure of the inner ring of the human nuclear pore complex (32 copies of Nup205) Deposited 2016-03-02	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 × 208 PDB declaration: 208-meric	Chain C 1–819（819 aa） Chain I 1–819（819 aa） Chain O 1–819（819 aa） Chain U 1–819（819 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 21.40 Å
5IJO Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) Deposited 2016-03-02	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 × 208 PDB declaration: 208-meric	Chain C 1–819（819 aa） Chain I 1–819（819 aa） Chain O 1–819（819 aa） Chain U 1–819（819 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 21.40 Å
7MW1 Crystal structure of the Homo sapiens NUP93-NUP53 complex (NUP93 residues 174-819; NUP53 residues 84-150) Deposited 2021-05-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 174–819（646 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.075 M TRIS pH 8.5, 17% (w/v) PEG 20000	Resolution 3.40 Å R-free 0.276
7MW1 Crystal structure of the Homo sapiens NUP93-NUP53 complex (NUP93 residues 174-819; NUP53 residues 84-150) Deposited 2021-05-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 174–819（646 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.075 M TRIS pH 8.5, 17% (w/v) PEG 20000	Resolution 3.40 Å R-free 0.276
7PER Model of the inner ring of the human nuclear pore complex Deposited 2021-08-11	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 × 192 PDB declaration: 192-meric	Chain C 1–819（819 aa） Chain I 1–819（819 aa） Chain O 1–819（819 aa） Chain U 1–819（819 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane.	Resolution 35.00 Å
7R5J Human nuclear pore complex (dilated) Deposited 2022-02-10	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 × 808 PDB declaration: 808-meric	Chain A0 1–819（819 aa） Chain A1 1–819（819 aa） Chain A2 1–819（819 aa） Chain A3 1–819（819 aa） Chain A4 1–819（819 aa） Chain A5 1–819（819 aa） Chain A6 1–819（819 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 50.00 Å
7R5K Human nuclear pore complex (constricted) Deposited 2022-02-10	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 × 808 PDB declaration: 808-meric	Chain A0 1–819（819 aa） Chain A1 1–819（819 aa） Chain A2 1–819（819 aa） Chain A3 1–819（819 aa） Chain A4 1–819（819 aa） Chain A5 1–819（819 aa） Chain A6 1–819（819 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.00 Å

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUP93_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 27–672； UniProt 174–819

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	7mw0
Deposition date deposition_date	2021-05-15
Structure title title	Crystal structure of Homo sapiens NUP93 solenoid (residues 174-819)
Keywords keywords	nuclear pore complex, nucleocytoplasmic transport, alpha-helical solenoid, nuclear pore, 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	39.67 Å
Radius of gyration Rg (electron density) rg_electron	40.70 Å
Forward intensity I(0) i0	79376800.00
Molecular weight molecular_weight	71999.0 kDa
Excluded volume excluded_volume	90359 Å³
Envelope volume envelope_volume	120200 Å³
Hydration-shell volume shell_volume	29598 Å³
Envelope diameter envelope_diameter	145.4 Å
Shell Rg shell_rg	37.43 Å
Envelope Rg envelope_rg	40.83 Å
Shape Rg shape_rg	40.71 Å
Total Rg total_rg	40.48 Å
Total atoms total_atoms	10124
Residues n_residues	624
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	147.3 Å
Rg (real space) rg_real	40.83 Å
Rg uncertainty (real space) rg_real_error	1.99 Å
I(0) (real space) i0_real	7.9380e+07
I(0) uncertainty (real space) i0_real_error	1.6660e+06
Rg (reciprocal space) rg_reciprocal	40.12 Å
I(0) (reciprocal space) i0_reciprocal	79320000.0000
Solution quality estimate total_estimate	0.6459
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.682
Kurtosis Kurtosis kurtosis	-0.393
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11190000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.215; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.062; Smooth: 0.686

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Nuclear pore complex protein Nup93
Molecular weight formula_weight	76831.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10316

SSGLNDIFEAQKIEWHEGSAGGSGGSGRSSLDNIEMAYARQIYIYNEKIVNGHLQPNLVDLCASVAELDDKSISDMWTMVKQMTDVLLTPATDALKNRSSVEVRMEFVRQALAYLEQSYKNYTLVTVFGNLHQAQLGGVPGTYQLVRSFLNIKLPAPLPGLQDGEVEGHPVWALIYYCMRCGDLLAASQVVNRAQHQLGEFKTWFQEYMNSKDRRLSPATENKLRLHYRRALRNNTDPYKRAVYCIIGRCDVTDNQSEVADKTEDYLWLKLNQVCFDDDGTSSPQDRLTLSQFQKQLLEDYGESHFTVNQQPFLYFQVLFLTAQFEAAVAFLFRMERLRCHAVHVALVLFELKLLLKSSGQSAQLLSHEPGDPPCLRRLNFVRLLMLYTRKFESTDPREALQYFYFLRDEKDSQGENMFLRCVSELVIESREFDMILGKLENDGSRKPGVIDKFTSDTKPIINKVASVAENKGLFEEAAKLYDLAKNADKVLELMNKLLSPVVPQISAPQSNKERLKNMALSIAERYRAQGISANKFVDSTFYLLLDLITFFDEYHSGHIDRAFDIIERLKLVPLNQESVEERVAAFRNFSDEIRHNLSEVLLATMNILFTQFKRLKGTSPSSSSRPQRVIEDRDSQLRSQARTLITFAGMIPYRTSGDTNARLVQMEVLMN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

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8. Citations (1)

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Unit-cell length a length_a	74.870 Å
Unit-cell length b length_b	66.070 Å
Unit-cell length c length_c	79.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2262
R_work r_work	0.2249
R_free r_free	0.2544

fit	/app/data/saxs_computation/mw/7mw0/7mw0.fit
pddf	/app/data/pr_computation/mw/7mw0/7mw0.pr.out
profile	/app/data/saxs_computation/mw/7mw0/7mw0.dat

Crystal structure of Homo sapiens NUP93 solenoid (residues 174-819)

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

Nuclear pore complex protein Nup93

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