SAXSdb — 1fio

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

SSO1 PROTEIN

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 31–225	Fragment：CYTOPLASMIC DOMAIN	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Hepes, PEG 4000, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.265

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 1FIO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3B5N Structure of the yeast plasma membrane SNARE complex Deposited 2007-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 189–257（69 aa） Fragment：Residues 189-257	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.25；298 K；100 mM MES pH 6.25, 30 % MPD, 200 mM Sodium bromide, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.60 Å R-free 0.248
3B5N Structure of the yeast plasma membrane SNARE complex Deposited 2007-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 189–257（69 aa） Fragment：Residues 189-257	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.25；298 K；100 mM MES pH 6.25, 30 % MPD, 200 mM Sodium bromide, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.60 Å R-free 0.248
3B5N Structure of the yeast plasma membrane SNARE complex Deposited 2007-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain J 189–257（69 aa） Fragment：Residues 189-257	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.25；298 K；100 mM MES pH 6.25, 30 % MPD, 200 mM Sodium bromide, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.60 Å R-free 0.248
9CRU Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 1 Deposited 2024-07-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain K 1–265（265 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain K 1–265（265 aa） Fragment：cytoplasmic domain	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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain K 1–265（265 aa） Fragment：cytoplasmic domain	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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain K 1–265（265 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain K 1–265（265 aa） Fragment：residues 1-265	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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain K 1–265（265 aa） Fragment：residues 1-265	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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain K 1–265（265 aa） Fragment：residues 1-265	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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain K 1–265（265 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain K 1–265（265 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

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

View Construct and Data Evidence

UniProt name	SSO1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–196； UniProt 31–225

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	1fio
Deposition date deposition_date	2000-08-04
Structure title title	CRYSTAL STRUCTURE OF YEAST T-SNARE PROTEIN SSO1
Keywords keywords	four helix bundle, alpha helix, MEMBRANE PROTEIN; MEMBRANE 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	22.67 Å
Radius of gyration Rg (electron density) rg_electron	22.20 Å
Forward intensity I(0) i0	9933810.00
Molecular weight molecular_weight	22217.0 kDa
Excluded volume excluded_volume	27338 Å³
Envelope volume envelope_volume	34856 Å³
Hydration-shell volume shell_volume	14899 Å³
Envelope diameter envelope_diameter	85.2 Å
Shell Rg shell_rg	26.53 Å
Envelope Rg envelope_rg	22.92 Å
Shape Rg shape_rg	22.13 Å
Total Rg total_rg	23.02 Å
Total atoms total_atoms	1555
Residues n_residues	190
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	87.2 Å
Rg (real space) rg_real	22.98 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	9.9340e+06
I(0) uncertainty (real space) i0_real_error	1.5720e+05
Rg (reciprocal space) rg_reciprocal	22.91 Å
I(0) (reciprocal space) i0_reciprocal	9933000.0000
Solution quality estimate total_estimate	0.7308
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.5 Å
Skewness Skewness skewness	0.645
Kurtosis Kurtosis kurtosis	-0.107
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2922000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.402; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.291; Smooth: 0.999

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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	SSO1 PROTEIN
Molecular weight formula_weight	22798.4 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	1708

MHDFVGFMNKISQINRDLDKYDHTINQVDSLHKRLLTEVNEEQASHLRHSLDNFVAQATDLQFKLKNEIKSAQRDGIHDTNKQAQAENSRQRFLKLIQDYRIVDSNYKEENKEQAKRQYMIIQPEATEDEVEAAISDVGGQQIFSQALLNANRRGEAKTALAEVQARHQELLKLEKSMAELTQLFNDMEELVIEQQ

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1fioa_
Class class	a — All alpha proteins
Fold Fold fold	a.47 — STAT-like
Superfamily Superfamily superfamily	a.47.2 — t-snare proteins
Family Family family	a.47.2.1 — t-snare proteins

CATH v4.4 (1 domains)

Domain ID domain_id	1fioA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	70 —

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8. Citations (1)

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Unit-cell length a length_a	42.517 Å
Unit-cell length b length_b	49.855 Å
Unit-cell length c length_c	113.840 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	2.100 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2210
R_work r_work	0.2190
R_free r_free	0.2650

fit	/app/data/saxs_computation/fi/1fio/1fio.fit
pddf	/app/data/pr_computation/fi/1fio/1fio.pr.out
profile	/app/data/saxs_computation/fi/1fio/1fio.dat

CRYSTAL STRUCTURE OF YEAST T-SNARE PROTEIN SSO1

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

SSO1 PROTEIN

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