SAXSdb — 7wo9

▼

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

Nucleoporin NUP188

OrganismNot specified

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 1–1655	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.81 Å

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 7WO9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 136 PDB declaration: 136-meric	Chain X 1–1655（1655 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 oligomeric state Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain X 1–1655（1655 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 oligomeric state Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain X 1–1655（1655 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
7N85 Inner ring spoke from the isolated yeast NPC Deposited 2021-06-13	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric	Chain N 1–1655（1655 aa） Chain P 1–1655（1655 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 structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain N 1–1655（1655 aa） Chain P 1–1655（1655 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 structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain N 1–1655（1655 aa） Chain P 1–1655（1655 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 conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric	Chain N 1–1655（1655 aa） Chain P 1–1655（1655 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 conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric	Chain N 1–1655（1655 aa） Chain P 1–1655（1655 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 conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric	Chain N 1–1655（1655 aa） Chain P 1–1655（1655 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 oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain E 1–1655（1655 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain E 1–1655（1655 aa） Chain Q 1–1655（1655 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 conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric	Chain N 1–1655（1655 aa） Chain P 1–1655（1655 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 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NU188_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1655； UniProt 1–1655

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7wo9
Deposition date deposition_date	2022-01-20
Structure title title	Cryo-EM structure of full-length Nup188
Keywords keywords	Nup188, cryo-EM, Saccharomyces cerevisiae, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	48.86 Å
Radius of gyration Rg (electron density) rg_electron	49.58 Å
Forward intensity I(0) i0	420829000.00
Molecular weight molecular_weight	180480.0 kDa
Excluded volume excluded_volume	230920 Å³
Envelope volume envelope_volume	341550 Å³
Hydration-shell volume shell_volume	62649 Å³
Envelope diameter envelope_diameter	183.9 Å
Shell Rg shell_rg	47.49 Å
Envelope Rg envelope_rg	49.53 Å
Shape Rg shape_rg	49.55 Å
Total Rg total_rg	49.60 Å
Total atoms total_atoms	12743
Residues n_residues	1581
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

▼

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

Maximum dimension Dmax dmax	173.5 Å
Rg (real space) rg_real	49.64 Å
Rg uncertainty (real space) rg_real_error	2.22 Å
I(0) (real space) i0_real	4.2080e+08
I(0) uncertainty (real space) i0_real_error	8.9190e+06
Rg (reciprocal space) rg_reciprocal	48.87 Å
I(0) (reciprocal space) i0_reciprocal	420400000.0000
Solution quality estimate total_estimate	0.7914
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.8 Å
Skewness Skewness skewness	0.652
Kurtosis Kurtosis kurtosis	-0.105
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35300000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.659; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.815; Smooth: 0.491

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Description description	Nucleoporin NUP188
Molecular weight formula_weight	188753.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	12743

MATPSFGNSSPQLTFTHVANFMNDAAADVSAVDAKQLAQIRQFLKANKTNLIESLNTIRQNVTSSGDHNKLRSTIANLLQINVDNDPFFAQSEDLSHAVEFFMSERSSRLHIVYSLLVNPDIDLETYSFIDNDRFNVVGKLISIISSVIQNYDIITASSLAHDYNNDQDMFTIVSLVQLKKFSDLKFILQILQILNLMILNTKVPVDIVNQWFLQYQNQFVEFCRNINSTDKSIDTSSLQLYKFQNFQDLSYLSETLISRISSLFTITTILILGLNTSIAQFDIQSPLYMDTETFDTVNSALENDVATNIVNEDPIFHPMIHYSWSFILYYRRALQSSESFDDSDITKFALFAESHDVLQKLNTLSEILSFDPVYTTVITVFLEFSLNFIPITASTSRVFAKIISKAPEQFIENFLTNDTFEKKLSIIKAKLPLLNESLIPLINLALIDTEFANFELKDICSFAVTKSSLNDLDYDLIADTITNSSSSSDIIVPDLIELKSDLLVAPPLENENSNCLLSIPKSTKGKILTIKQQQQQQQQQNGQQPPTTSNLIIFLYKFNGWSLVGRILQNLLHSYMEKGTQLDDLQHELMISIIKLVTNVVDPKTSIEKSSEILSYLSNSLDTSASTINGASIIQVIFEIFEISLQRKDYTSIVQCCEFMTMLTPNYLHLVSSYLNKSDLLDKYGKTGLSNMILGSVELSTGDYTFTIQLLKLTKVFIRESLSLKNIHISKRSKIDIINKLILHAIHIFESYYNWKYNNFLQKFEIAFHLTLIFYDVLHDVFTINPHQKDQLIISSSANKLLQLFLTPMDSIDLAPNTLTNILISPLNTTTKILGDKILGNLYSKVMNNSFKLCTLLIAIRGSNRDLKPSNLEKLLFINSSKLVDVYTLPSYVHFKVQIIELLSYLVEAPWNDDYPFLLSFLGEAKSMAFLKEVLSDLSSPVQDWNLLRSLYIFFTTLLESKQDGLSILFLTGQFASNKKINDESSIDKKSSILTVLQKNSLLLDSTPEEVSCKLLETITYVLNTWTNSKIFIKDPKFVNSLLAKLKDSKKLFQKKENLTRDETVSLIKKYKLISRIVEIFALCIYNSTDSNSEILNFLNQEDLFELVHHFFQIDGFNKTFHDELNLKFKEKWPSLELQSFQKIPLSRINENENFGYDIPLLDIVLKADRSWNEPSKSQTNFKEEITDASLNLQYVNYEISTAKAWGALITTFVKRSTVPLNDGFVDLVEHFLKLNIDFGSDKQMFTQIYLERIELSFYILYSFKLSGKLLKEEKIIELMNKIFTIFKSGEIDFIKNIGKSLKNNFYRPLLRSVLVLLELVSSGDRFIELISDQLLEFFELVFSKGVYLILSEILCQINKCSTRGLSTDHTTQIVNLEDNTQDLLLLLSLFKKITNVNPSKNFNVILASSLNEVGTLKVILNLYSSAHLIRINDEPILGQITLTFISELCSIEPIAAKLINSGLYSVLLESPLSVAIQQGDIKPEFSPRLHNIWSNGLLSIVLLLLSQFGIKVLPETCLFVSYFGKQIKSTIYNWGDNKLAVSSSLIKETNQLVLLQKMLNLLNYQELFIQPKNSDDQQEAVELVIGLDSEHDKKRLSAALSKFLTHPKYLNSRIIPTTLEEQQQLEDESSRLEFVKGISRDIKALQDSLFKDV

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.81 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	607216

fit	/app/data/saxs_computation/wo/7wo9/7wo9.fit
pddf	/app/data/pr_computation/wo/7wo9/7wo9.pr.out
profile	/app/data/saxs_computation/wo/7wo9/7wo9.dat

Cryo-EM structure of full-length Nup188

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

Nucleoporin NUP188

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)