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9yrm

CryoEM Structure of VPS13 protein, 1-1390 from C. thermophilum, in complex with calmodulin

Method: ELECTRON MICROSCOPY D_max: 138.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yrm
deposition_date	2025-10-16
title	CryoEM Structure of VPS13 protein, 1-1390 from C. thermophilum, in complex with calmodulin
keywords	lipid transport protein; BLTP, 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	40.75 Å
rg_electron	40.53 Å
i0	251401000.00
molecular_weight	129340.0 kDa
excluded_volume	162570 Å³
envelope_volume	249710 Å³
shell_volume	53956 Å³
envelope_diameter	144.1 Å
shell_rg	44.18 Å
envelope_rg	39.11 Å
shape_rg	40.53 Å
total_rg	40.77 Å
total_atoms	9116
n_residues	1128
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	138.1 Å
rg_real	40.76 Å
rg_real_error	1.61 Å
i0_real	2.5140e+08
i0_real_error	4.2940e+06
rg_reciprocal	40.75 Å
i0_reciprocal	251400000.0000
total_estimate	0.8715
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.6 Å
skewness	0.364
kurtosis	-0.170
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	15650000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.870

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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	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9116

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Entity 2 polymer

description	Intermembrane lipid transfer protein VPS13
formula_weight	162183.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MDYKDHDGDYKDHDIDYKDDDDKLAAAMLEGLVAGLLNRFLGMYVKNFDPKQLKWEVWNGKVRLDNLELQREALDQLKLPINVIKGHLGHLVLHIPWKTLASEQVKINIEDVFLLASPKEEAEYDEDEEARRRHRLKMEKLDSAELLKERSQEGLSEEEQKRTQTFAQALVTKIVDNLQITIRNIHIRYEDAISAPGHPFALGITLEEFSAVSTDSDWTPAFITSIQSAHKLATLESLAIYWDTDAKLIGPGREPHEHSDQIPHDEMLKFFREMIAKGEADLSSEHQFILKPVSGQAKIEIDKTGSHTVPRYKANLLFDEIGVVLDDQQYRDALMMVDLFHYFIRHQEYKKFQPKGVTPKEDPRAWFRFAGNAVLSKIHERNRRWSWDYFRERRDDRRRYIELFKKTKQNIQLTPEEREDLDKLEWKLSYEDLRFWRSLARNQLKKENAEALKNKPPPQPQQQQGWLSWVWGSKPVQPQQEEQQGDENTRITEAQRKELYEVIQWDEKAALAAEIDVPRDSVRLLIETSLSTGSFTLRQNPHGDARDLISLHFDLFRAKGLTRPDSFLIDISLGGFRVNDNTTPDSLYKEIVRVKDAPNTEGQKRYSIADLELTVDEEAFFELQVEQHPLDGQGDVAVTMKLKPLEIIWNPNVVVGIADFFRPPERHMESINALLETANATVEGLRAQTRAGLQFALEEHKTVNAKLDLQAPLIILPESITTPNSTCLIVDAGHISVNSELVDKETMKQVQSTQDRPCTEEDLRRLEELMYDRFLVKLTSTQVLIGPSVEITKQQLVQRDEKRQLHIVDQINLDFVVAMSILPKAPNLTKLKISGHLPVLQVNASDSKYKHLMRIIEVAIPKLYDVEPVLAPSGSHPTIRPRLASDASTRSRRASFRKASTQFLQFVSQQQEIVLDESDSDDDSEKFEDAKDTSVDEQLRIQQRIFDFKFTVDQLRGSLYRSDPEGKHPDQLLVELVAENFGVEYHLRPYDMSAMVSLGSVTMDDFVENPPAEFKSIVSSGDIEDRKQARDLVRVKFVRVKKESPEFMSVYDGIETNVDVAISTINLVVTRKTLLTLLDFILVTFSNPQPAAPVATRMAVTDQESETNIIVQPPPIESGPIRVKVDLKSIRMILNNDGIRLATLSFNHADVGVYILGRYMRVSAKLGDLSLVDDVNLGVSEDSSLRQLVTIQGNELADFRYEYFDPDKPEKNPGYDSSIYLRAGSVKVNFIEEPFRKIVDFLVKFGKMQAIYNAARMAAANQAQQLQQSQSRIKFDIVVKTPIVVFPRVVMSPKPKRDVITAYLGEIYAQNAFVPLDDSEKADMAMKLTTGIRNIRLTSHFHYSEGRDEVLELIDHVDLGFTIIYAEHKEGIKRPDLEIEGSMSDFNLRITPYQLSALLAISQSVPTVFAADVEQHT

Source

organism	Thermochaetoides thermophila
ncbi_taxonomy_id	209285
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	3.75 Å
resolution_method	—
num_particles	175364

fit	/app/data/saxs_computation/yr/9yrm/9yrm.fit
pddf	/app/data/pr_computation/yr/9yrm/9yrm.pr.out
profile	/app/data/saxs_computation/yr/9yrm/9yrm.dat

CryoEM Structure of VPS13 protein, 1-1390 from C. thermophilum, in complex with calmodulin

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

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)