SAXSdb — 9nud

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

Vesicular-fusion protein SEC18

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–758 Chain B； UniProt 1–758 Chain C； UniProt 1–758 Chain D； UniProt 1–758 Chain E； UniProt 1–758 Chain F； UniProt 1–758	Not recorded	MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.38 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 9NUD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CR5 N-TERMINAL DOMAIN OF SEC18P Deposited 1999-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–210（189 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	NEN 1-ETHYL-PYRROLIDINE-2,5-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 8000, sodium phosphate, dimethyl sulfoxide, ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.30 Å R-free 0.277
1CR5 N-TERMINAL DOMAIN OF SEC18P Deposited 1999-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–210（189 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	NEN 1-ETHYL-PYRROLIDINE-2,5-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 8000, sodium phosphate, dimethyl sulfoxide, ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.30 Å R-free 0.277
1CR5 N-TERMINAL DOMAIN OF SEC18P Deposited 1999-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 22–210（189 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	NEN 1-ETHYL-PYRROLIDINE-2,5-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 8000, sodium phosphate, dimethyl sulfoxide, ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.30 Å R-free 0.277
9CRU Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 1 Deposited 2024-07-22	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.89 Å
9CRX Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 3 Deposited 2024-07-22	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
9N22 Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 2 Deposited 2025-01-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å
9NG2 Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 4 Deposited 2025-02-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.61 Å
9NLU Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 5 Deposited 2025-03-03	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.29 Å
9NLW Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 6 Deposited 2025-03-03	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
9NLY Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 7 Deposited 2025-03-03	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.75 Å
9NLZ Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 8 Deposited 2025-03-03	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.13 Å
9NM1 Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - All Merge (Class 9, focused on D1/D2) Deposited 2025-03-03	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9NUE Y20S after Mg2+ (Sec18) - Class 3 Deposited 2025-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa） Chain G 1–758（758 aa）	Not recorded	MG MAGNESIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å
9NUZ Y20S after Mg2+ (Sec18) - Class 4 Deposited 2025-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa） Chain G 1–758（758 aa）	Not recorded	MG MAGNESIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9NV0 Sec18 Mg2+ class 2 Deposited 2025-03-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.83 Å
9NV1 Sec18 Mg2+ class 1 Deposited 2025-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa） Chain G 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å

14 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SEC18_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–761； UniProt 1–758 Author chain B； PDBConstruct 4–761； UniProt 1–758 Author chain C； PDBConstruct 4–761； UniProt 1–758 Author chain D； PDBConstruct 4–761； UniProt 1–758 Author chain E； PDBConstruct 4–761； UniProt 1–758 Author chain F； PDBConstruct 4–761； UniProt 1–758

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	9nud
Deposition date deposition_date	2025-03-19
最后修订 last_revision	2025-10-01
Structure title title	Y20S after Mg2+ (Sec18) - Class 2
Keywords keywords	SNARE, NSF, Sec18, AAA+, TRANSLOCASE; TRANSLOCASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	50.68 Å
Radius of gyration Rg (electron density) rg_electron	49.95 Å
Forward intensity I(0) i0	1660070000.00
Molecular weight molecular_weight	337220.0 kDa
Excluded volume excluded_volume	421970 Å³
Envelope volume envelope_volume	670270 Å³
Hydration-shell volume shell_volume	107850 Å³
Envelope diameter envelope_diameter	155.6 Å
Shell Rg shell_rg	58.00 Å
Envelope Rg envelope_rg	47.94 Å
Shape Rg shape_rg	49.95 Å
Total Rg total_rg	50.25 Å
Total atoms total_atoms	23618
Residues n_residues	2987
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	154.8 Å
Rg (real space) rg_real	50.41 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	1.6600e+09
I(0) uncertainty (real space) i0_real_error	3.0210e+07
Rg (reciprocal space) rg_reciprocal	50.90 Å
I(0) (reciprocal space) i0_reciprocal	1661000000.0000
Solution quality estimate total_estimate	0.8902
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	64.9 Å
Skewness Skewness skewness	0.005
Kurtosis Kurtosis kurtosis	-0.597
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	147400000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.810

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Vesicular-fusion protein SEC18
Molecular weight formula_weight	84423.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	23663

GAHMFKIPGFGKAAANHTPPDMTNMDTRTRHLKVSNCPNNSYALANVAAVSPNDFPNNIYIIIDNLFVFTTRHSNDIPPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFRARGKAVSTVFDQDELAKQFVRCYESQIFSPTQYLIMEFQGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINFFKGRDGLVNLKSSNSLRPRSNAVIRPDFKFEDLGVGGLDKEFTKIFRRAFASRIFPPSVIEKLGISHVKGLLLYGPPGTGKTLIARKIGTMLNAKEPKIVNGPEILSKYVGSSEENIRNLFKDAEAEYRAKGEESSLHIIIFDELDSVFKQRGSRGDGTGVGDNVVNQLLAKMDGVDQLNNILVIGMTNRKDLIDSALLRPGRFEVQVEIHLPDEKGRLQIFDIQTKKMRENNMMSDDVNLAELAALTKNFSGAEIEGLVKSASSFAINKTVNIGKGATKLNTKDIAKLKVTREDFLNALNDVTPAFGISEEDLKTCVEGGMMLYSERVNSILKNGARYVRQVRESDKSRLVSLLIHGPAGSGKTALAAEIALKSGFPFIRLISPNELSGMSESAKIAYIDNTFRDAYKSPLNILVIDSLETLVDWVPIGPRFSNNILQMLKVALKRKPPQDRRLLIMTTTSAYSVLQQMDILSCFDNEIAVPNMTNLDELNNVMIESNFLDDAGRVKVINELSRSCPNFNVGIKKTLTNIETARHDEDPVNELVELMTQSA

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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8. Citations (1)

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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	3.38 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	86542

fit	/app/data/saxs_computation/nu/9nud/9nud.fit
pddf	/app/data/pr_computation/nu/9nud/9nud.pr.out
profile	/app/data/saxs_computation/nu/9nud/9nud.dat

Y20S after Mg2+ (Sec18) - Class 2

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

Vesicular-fusion protein SEC18

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