SAXSdb — 9vmp

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1. Structure Basics

entry_id	9vmp
deposition_date	2025-06-28
title	Cryo-EM structure of the A-1-OXGR1-Gq complex
keywords	OXGR1, Gq, A-1, MEMBRANE PROTEIN/IMMUNE SYSTEM, MEMBRANE PROTEIN-IMMUNE SYSTEM complex; MEMBRANE PROTEIN/IMMUNE SYSTEM
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	36.08 Å
rg_electron	35.79 Å
i0	414503000.00
molecular_weight	111060.0 kDa
excluded_volume	107900 Å³
envelope_volume	186080 Å³
shell_volume	44338 Å³
envelope_diameter	119.6 Å
shell_rg	40.82 Å
envelope_rg	35.90 Å
shape_rg	35.82 Å
total_rg	35.98 Å
total_atoms	8406
n_residues	1132
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	117.3 Å
rg_real	36.03 Å
rg_real_error	0.82 Å
i0_real	4.1450e+08
i0_real_error	6.3940e+06
rg_reciprocal	36.06 Å
i0_reciprocal	414500000.0000
total_estimate	0.8984
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.0 Å
skewness	0.192
kurtosis	-0.614
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0001
highest_alpha	34000000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.911

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Guanine nucleotide-binding protein G(q) subunit alpha isoforms short
formula_weight	41244.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8406

TLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVNGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLSVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYNLV

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	37069.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

LDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
formula_weight	5818.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

ARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	2-oxoglutarate receptor 1
formula_weight	33758.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

DENIPLKMHYLPVIYGIIFLVGFPGNAVVISTYIFKMRPWKSSTIIMLNLACTDLLYLTSLPFLIHYYASGENWIFGDFMCKFIRFSFHFNLYSSILFLTCFSIFRYCVIIHPMSCFSIHKTRCAVVACAVVWIISLVAVIPMTFLITSTNRTNRSACLDLTSSDELNTIKWYNLILTATTFCLPLVIVTLCYTTIIHTLTHGLQTDSCLKQKARRLTILLLLAFYVCFLPFHILRVIRIESRLLSISCSIENQIHEAYIVSRPLAALNTFGNLLLYVVVSDNFQQAVCSTVRCK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	scFv16
formula_weight	26164.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLE

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Spodoptera frugiperda

Entity 6 non-polymer

description	methyl N-[(3S)-1,1-bis(oxidanylidene)-2,3-dihydrothiophen-3-yl]carbamate
formula_weight	191.2 kDa
src_method	syn
entity_count	1

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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	2.50 Å
resolution_method	—
num_particles	357271

fit	/app/data/saxs_computation/vm/9vmp/9vmp.fit
pddf	/app/data/pr_computation/vm/9vmp/9vmp.pr.out
profile	/app/data/saxs_computation/vm/9vmp/9vmp.dat

Cryo-EM structure of the A-1-OXGR1-Gq complex

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 (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)