SAXSdb — 9umg

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1. Structure Basics

entry_id	9umg
deposition_date	2025-04-21
title	Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)
keywords	Transporter, Complex, polyP synthesis, Vacuolar membrane, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	43.63 Å
rg_electron	44.44 Å
i0	259342000.00
molecular_weight	140140.0 kDa
excluded_volume	178890 Å³
envelope_volume	249910 Å³
shell_volume	49049 Å³
envelope_diameter	156.8 Å
shell_rg	46.20 Å
envelope_rg	43.85 Å
shape_rg	44.46 Å
total_rg	44.43 Å
total_atoms	9877
n_residues	1200
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	150.4 Å
rg_real	44.02 Å
rg_real_error	2.04 Å
i0_real	2.5930e+08
i0_real_error	5.0870e+06
rg_reciprocal	43.63 Å
i0_reciprocal	259200000.0000
total_estimate	0.7997
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.6 Å
skewness	0.474
kurtosis	-0.573
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	47300000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.658; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.665; Smooth: 0.753

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Vacuolar transporter chaperone complex subunit 1
formula_weight	13253.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9877

PLLQRTPGKKIALPTRVEPKVFFANERTFLSWLNFTVMLGGLGVGLLNFGDKIGRVSAGLFTFVAMGTMIYALVTYHWRAAAIRRRGSGPYDDRLGPTLLCFFLLVAVIINFILRLKY

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 2 polymer

description	Vacuolar transporter chaperone complex subunit 1
formula_weight	11592.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,C

VEPKVFFANERTFLSWLNFTVMLGGLGVGLLNFGDKIGRVSAGLFTFVAMGTMIYALVTYHWRAAAIRRRGSGPYDDRLGPTLLCFFLLVAVIINFILRLKYN

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 3 polymer

description	Vacuolar transporter chaperone complex subunit 4
formula_weight	60283.6 kDa
ec_number	2.7.4.1
mutation	R264A,R266A,E426A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

RQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLRKDEGAEAHALAWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLNVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLPQMDVDIRKPPLPTNIEITRPGRSDNEDNDFDEDDEDDAALVAAMTNAPGNSLDIEESVGYGATSAPTSNTNHVVESANAAYYQRKIRNAENPISKKYYEIVAFFDHYFNGDQISKIPKGTTFDTQIRAPPGKTICVPVRVEPKVYFATERTYLSWLSISILLGGVSTTLLTYGSPTAMIGSIGFFITSLAVLIRTVMVYAKRVVNIRLKRAVDYEDKIGPGMVSVFLILSILFSFFCNLVAKL

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 4 polymer

description	Vacuolar transporter chaperone 3 complex subunit 3
formula_weight	69612.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

ASFKSYKFWVHDDNIMEVKARILRHLPALVYASVPNENDDFVDNLESDVRVQPEARLNIGSKSNSLSSDGNSNQDVEIGKSKSVIFPQSYDPTITTLYFDNDFFDLYNNRLLKISGAPTLRLRWIGKLLDKPDIFLEKRTFTENTETGNSSFEEIRLQMKAKFINNFIFKNDPSYKNYLINQLRERGTQKEELEKLSRDFDNIQNFIVEEKLQPVLRATYNRTAFQIPGDQSIRVTIDSNIMYIREDSLDKNRPIRNPENWHRDDIDSNIPNPLRFLRAGEYSKFPYSVMEIKVINQDNSQMPNYEWIKDLTNSHLVNEVPKFSLYLQGVASLFGEDDKYVNILPFWLPDLETDIRKNPQEAYEEEKKTLQKQKSIHDKLDNMRRLSKISVPDGKTTERQGQKDQNTRHVIADLEDHESSDEEGTALPKKSAVKKGKKFKTNAAFLKILAGKNISENGNDPYSDDTDSASSFQLPPGVKKPVHLLKNAGPVKVEAKVWLANERTFNRWLSVTTLLSVLTFSIYNSVQKAEFPQLADLLAYVYFFLTLFCGVWAYRTYLKRLTLIKGRSGKHLDAPVGPILVAVVLIVTLVVNFSVAFKEAARRE

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 5 polymer

description	Vacuole transporter chaperone complex subunit 5
formula_weight	12434.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

SIYEYRHDEVVTFLYLSALLTSCIMASVCLGIVLSLFRGQSNNEIDLEIQNILIAIIIISLLVSLILICACLLLLFSRFTLAPIWHYVGCFTMFFSVTGTVCYGMIEIFF

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 6 non-polymer

description	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	3

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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	3.040 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.04 Å
resolution_method	—
num_particles	186553

fit	/app/data/saxs_computation/um/9umg/9umg.fit
pddf	/app/data/pr_computation/um/9umg/9umg.pr.out
profile	/app/data/saxs_computation/um/9umg/9umg.dat

Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)

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

Refinement

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)