SAXSdb — 9y48

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

Lethal(2) giant larvae protein homolog SRO7

Saccharomyces cerevisiae

UniProt Q12038

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 1–1033	Not recorded	NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.10 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 9Y48	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OAJ Crystal structure of Sro7 from S. cerevisiae Deposited 2006-12-15	Different construct 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 61–962（902 aa）	Not recorded	ZN ZINC ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；40 mM MES pH 6.5, 12% PEG 3350, 200 mM ammonium fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.40 Å R-free 0.262

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SRO7_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1033； UniProt 1–1033

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	9y48
Deposition date deposition_date	2025-09-02
Structure title title	Sro7 bound to His-Exo84 (1-326) on a Nickel-NTA lipid monolayer
Keywords keywords	Exocytosis, membrane trafficking, vesicle tethering; EXOCYTOSIS
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	33.15 Å
Radius of gyration Rg (electron density) rg_electron	32.62 Å
Forward intensity I(0) i0	139274000.00
Molecular weight molecular_weight	97027.0 kDa
Excluded volume excluded_volume	122690 Å³
Envelope volume envelope_volume	156370 Å³
Hydration-shell volume shell_volume	40486 Å³
Envelope diameter envelope_diameter	112.7 Å
Shell Rg shell_rg	39.01 Å
Envelope Rg envelope_rg	32.51 Å
Shape Rg shape_rg	32.61 Å
Total Rg total_rg	33.18 Å
Total atoms total_atoms	6831
Residues n_residues	875
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	109.5 Å
Rg (real space) rg_real	33.27 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.3930e+08
I(0) uncertainty (real space) i0_real_error	2.0830e+06
Rg (reciprocal space) rg_reciprocal	33.22 Å
I(0) (reciprocal space) i0_reciprocal	139300000.0000
Solution quality estimate total_estimate	0.8763
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.2 Å
Skewness Skewness skewness	0.400
Kurtosis Kurtosis kurtosis	-0.518
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0003
Highest regularization parameter α highest_alpha	34760000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.933

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Lethal(2) giant larvae protein homolog SRO7
Molecular weight formula_weight	114639.4 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	6831

MFGSKRLKNVKEAFKSLKGQNSETPIENSKASFKSKNSKTSTISKDAKSSSSLKIPISSNNKNKIFSLAETNKYGMSSKPIAAAFDFTQNLLAIATVTGEVHIYGQQQVEVVIKLEDRSAIKEMRFVKGIYLVVINAKDTVYVLSLYSQKVLTTVFVPGKITSIDTDASLDWMLIGLQNGSMIVYDIDRDQLSSFKLDNLQKSSFFPAARLSPIVSIQWNPRDIGTVLISYEYVTLTYSLVENEIKQSFIYELPPFAPGGDFSEKTNEKRTPKVIQSLYHPNSLHIITIHEDNSLVFWDANSGHMIMARTVFETEINVPQPDYIRDSSTNAAKISKVYWMCENNPEYTSLLISHKSISRGDNQSLTMIDLGYTPRYSITSYEGMKNYYANPKQMKIFPLPTNVPIVNILPIPRQSPYFAGCHNPGLILLILGNGEIETMLYPSGIFTDKASLFPQNLSWLRPLATTSMAASVPNKLWLGALSAAQNKDYLLKGGVRTKRQKLPAEYGTAFITGHSNGSVRIYDASHGDIQDNASFEVNLSRTLNKAKELAVDKISFAAETLELAVSIETGDVVLFKYEVNQFYSVENRPESGDLEMNFRRFSLNNTNGVLVDVRDRAPTGVRQGFMPSTAVHANKGKTSAINNSNIGFVGIAYAAGSLMLIDRRGPAIIYMENIREISGAQSACVTCIEFVIMEYGDDGYSSILMVCGTDMGEVITYKILPASGGKFDVQLMDITNVTSKGPIHKIDAFSKETKSSCLATIPKMQNLSKGLCIPGIVLITGFDDIRLITLGKSKSTHKGFKYPLAATGLSYISTVEKNNDRKNLTVIITLEINGHLRVFTIPDFKEQMSEHIPFPIAAKYITESSVLRNGDIAIRVSEFQASLFSTVKEQDTLAPVSDTLYINGIRIPYRPQVNSLQWARGTVYCTPAQLNELLGGVNRPASKYKESIIAEGSFSERSSDDNNANHPEHQYTKPTRKGRNSSYGVLRNVSRAVETRWDAVEDRFNDYATAMGETMNEAVEQTGKDVMKGALGF

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	Saccharomyces cerevisiae

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

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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	3.100 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	524737

fit	/app/data/saxs_computation/y4/9y48/9y48.fit
pddf	/app/data/pr_computation/y4/9y48/9y48.pr.out
profile	/app/data/saxs_computation/y4/9y48/9y48.dat

Sro7 bound to His-Exo84 (1-326) on a Nickel-NTA lipid monolayer

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

Lethal(2) giant larvae protein homolog SRO7

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)