SAXSdb — 9rs7

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1. Structure Basics

entry_id	9rs7
deposition_date	2025-06-30
title	Ypt7 in complex with its GEF Mon1-Ccz1
keywords	longin domain, GEF, nucleotide exchange, endosome, autophagosome, small GTPase, CYTOSOLIC PROTEIN; CYTOSOLIC 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	34.46 Å
rg_electron	33.80 Å
i0	201483000.00
molecular_weight	116920.0 kDa
excluded_volume	147600 Å³
envelope_volume	182550 Å³
shell_volume	45240 Å³
envelope_diameter	115.2 Å
shell_rg	40.17 Å
envelope_rg	33.79 Å
shape_rg	33.79 Å
total_rg	34.30 Å
total_atoms	8250
n_residues	1052
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	111.2 Å
rg_real	34.44 Å
rg_real_error	0.76 Å
i0_real	2.0150e+08
i0_real_error	3.1660e+06
rg_reciprocal	34.45 Å
i0_reciprocal	201500000.0000
total_estimate	0.8957
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	38.7 Å
skewness	0.299
kurtosis	-0.496
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	97620000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.873

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Rab small monomeric GTPase-like protein
formula_weight	23218.2 kDa
mutation	N125I
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	8250

GSMSSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSASYKATIGADFLTREVMVDDRQVTMQLWDTAGQERFQSLGVAFYRGADCCVLVFDVNNAKSFDALDSWRDEFLIQASPRDPENFPFVVLGIKIDVEESKRVISTKRAQTFCQSKGGIPYFETSAKEAINVEEAFQVIARNALMQEESEEFSGDFQDPINIHIENERDGCAC

Source

organism	Thermochaetoides thermophila
ncbi_taxonomy_id	209285
host_organism	Escherichia coli

Entity 2 polymer

description	Vacuolar fusion protein MON1
formula_weight	72198.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

GPLGSMTQNNAPESVAAEGTVAGQQTDTTKPEPSSQPAPEPPSQVTTDFPPNNKPNDVPATEPASSSPRPTEPPAPPPPKPTIALSPLDIATLTFPDGTRGTFPAPPQTSAQSVSTPSIASGHVTPQRDTDTASITSVAGTLRGVTGTAGDLASLLAGDGLGRKSKAWRVLRAQQQACGEGSGEEGEITEIEGLGLGEGMEGFERELDNIPDTLPDDERLALWKGKLKHYLILSSAGKPIWSRHGDLSLVNSTMGVVQTIISFYEGARNPLLGFTAGKVRFVILIKGPLYFVAISRLRESDAQLRAQLEALYMQILSTLTLPILTNIFAHRPSTDLRGPLQGTESLLASLADSFTKGSPSTLLSALECLRLRKSQRQAITNIFLKSRCEELLYGLLVAGGKLVSVIRPRKHSLHPSDLQLIFNMLFESGGIKGNGGENWIPLCLPAFNNTGYLYMYVSFLDDKAPDDQNQPPESSNLDASNKNSSNTPDDDLTALILISPSREAFYALQSMRTRLVSQLLSTGYLSLIRSTALSGRPSITSILPKTPLLHFLYKSRPNVQWCMSSLSSLTPPGATATETLLARRKLMSVYEELHAALHARHAHLRVVYSTADEKEGEGLACLGWSTPAFEVYCVAPGCVGRAGMAREVNRVVQWARREEERLFILGGGVF

Source

organism	Thermochaetoides thermophila
ncbi_taxonomy_id	209285
host_organism	Escherichia coli

Entity 3 polymer

description	CCZ1/INTU/HSP4 first Longin domain-containing protein
formula_weight	75867.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SMTTPVSPSPSGIIPAQLGFLAIYNPALGTTDETLEDQIVYYATASTLSQARRRHRRPRRRDRQRAQSVVKDSRPNAAGATGDSEAVAEDKDPVSKEERHERLRQIGLAQGMVEFAKSFSDGEPVDTIDTEKARVILVEVEEGWWILASIDLTRLPLPQIKTPTSSSAPPPAPNLNPLPPEPAYEYSSREVKPPSLLRADLLRAYDLFLLHHGSSLSSLLASQGRAQLVASLTRFWDHFLATWNVLLHGNPACDVFGGIKLAASGELGIGVGEEERGSGEREVLEGLVERVEGLVDVVVGRYGGPPSEKGPEEEQWLGLGGEVGEEDGAVFLGVGALDRKSLRGVVQWMEEVYVWGENAFGKPRRDLSTGHFLLGLSECSEEELTSSQANPKAIFVELKPSYQHPSRKIPPEDPQPLGKVGPELPRDHTARLRPVIYVSQPFIYILLFSEITPSPSTWPTLAESLHAQLSPLQKPLLHSTSYRPERPVVETTSSSGTTTQHQIFDLVYDTETLTLQSTIPNIPDPFPYSATTPTGHSTGQQHHQQSIWTRVEALQTHAQILAILSSGRAIPTDPSSFTHLPWEEGERTCKTARGWWIVWTRVVEHSPPDAVSLHHARDDDDNDDDASCSVLGHLRSVSSSHAAGSTSSSSGSGFGLGAIPGLGGLGGWAADGATRLAQGIGIDTRRYVEGLLTSLGR

Source

organism	Thermochaetoides thermophila
ncbi_taxonomy_id	209285
host_organism	Escherichia coli

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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	triclinic

resolution	3.00 Å
resolution_method	—
num_particles	524738

fit	/app/data/saxs_computation/rs/9rs7/9rs7.fit
pddf	/app/data/pr_computation/rs/9rs7/9rs7.pr.out
profile	/app/data/saxs_computation/rs/9rs7/9rs7.dat

Ypt7 in complex with its GEF Mon1-Ccz1

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)