SAXSdb — 9yg4

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1. Structure Basics

entry_id	9yg4
deposition_date	2025-09-27
title	VPS13A/Nt-CaM
keywords	VPS13A, Calmodulin, Complex, ER, LIPID TRANSPORT; LIPID TRANSPORT
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	34.35 Å
rg_electron	33.28 Å
i0	137431000.00
molecular_weight	95731.0 kDa
excluded_volume	121220 Å³
envelope_volume	179890 Å³
shell_volume	45591 Å³
envelope_diameter	107.3 Å
shell_rg	40.27 Å
envelope_rg	31.60 Å
shape_rg	33.28 Å
total_rg	33.95 Å
total_atoms	6741
n_residues	831
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	99.5 Å
rg_real	34.11 Å
rg_real_error	0.57 Å
i0_real	1.3740e+08
i0_real_error	2.0420e+06
rg_reciprocal	34.27 Å
i0_reciprocal	137400000.0000
total_estimate	0.9088
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	45.4 Å
skewness	-0.060
kurtosis	-0.589
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	6316000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Calmodulin-1
formula_weight	16852.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	6741

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Intermembrane lipid transfer protein VPS13A
formula_weight	92066.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MVFESVVVDVLNRFLGDYVVDLDTSQLSLGIWKGAVALKNLQIKENALSQLDVPFKVKVGHIGNLKLIIPWKNLYTQPVEAVLEEIYLLIVPSSRIKYDPLKEEKQLMEAKQQELKRIEEAKQKVVDQEQHLPEKQDTFAEKLVTQIIKNLQVKISSIHIRYEDDITNRDKPLSFGISLQNLSMQTTDQYWVPCLHDETEKLVRKLIRLDNLFAYWNVKSQMFYLSDYDNSLDDLKNGIVNENIVPEGYDFVFRPISANAKLVMNRRSDFDFSAPKINLEIELHNIAIEFNKPQYFSIMELLESVDMMAQNLPYRKFKPDVPLHHHAREWWAYAIHGVLEVNVCPRLWMWSWKHIRKHRQKVKQYKELYKKKLTSKKPPGELLVSLEELEKTLDVFNITIARQTAEVEVKKAGYKIYKEGVKDPEDNKGWFSWLWSWSEQNTNEQQPDVQPETLEEMLTPEEKALLYEAIGYSETAVDPTLLKTFEALKFFVHLKSMSIVLRENHQKPELVDIVIEEFSTLIVQRPGAQAIKFETKIDSFHITGLPDNSEKPRLLSSLDDAMSLFQITFEINPLDETVSQRCIIEAEPLEIIYDARTVNSIVEFFRPPKEVHLAQLTAATLTKLEEFRSKTATGLLYIIETQKVLDLKINLKASYIIVPQDGIFSPTSNLLLLDLGHLKVTSKSRSELPDVKQGEANLKEIMDRAYDSFDIQLTSVQLLYSRVGDNWREARKLSVSTQHILVPMHFNLELSKAMVFMDVRMPKFKIYGKLPLISLRISDKKLQGIMELIESIP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.38 Å
resolution_method	—
num_particles	464055

fit	/app/data/saxs_computation/yg/9yg4/9yg4.fit
pddf	/app/data/pr_computation/yg/9yg4/9yg4.pr.out
profile	/app/data/saxs_computation/yg/9yg4/9yg4.dat

VPS13A/Nt-CaM

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)