SAXSdb — 9vmg

▼

1. Structure Basics

entry_id	9vmg
deposition_date	2025-06-27
title	Cryo-EM structure of the spermine-bound sea lamprey TAAR348-Gs complex
keywords	GPCR, TAAR348, Spermine, Sea lamprey, MEMBRANE PROTEIN/IMMUNE SYSTEM, MEMBRANE PROTEIN-IMMUNE SYSTEM complex; MEMBRANE PROTEIN/IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	37.33 Å
rg_electron	37.22 Å
i0	301040000.00
molecular_weight	139700.0 kDa
excluded_volume	174320 Å³
envelope_volume	221830 Å³
shell_volume	50517 Å³
envelope_diameter	124.4 Å
shell_rg	42.33 Å
envelope_rg	37.24 Å
shape_rg	37.20 Å
total_rg	37.59 Å
total_atoms	9818
n_residues	1270
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

▼

3. P(r) Analysis (GNOM)

dmax	122.2 Å
rg_real	37.29 Å
rg_real_error	0.84 Å
i0_real	3.0100e+08
i0_real_error	5.0110e+06
rg_reciprocal	37.32 Å
i0_reciprocal	301000000.0000
total_estimate	0.9007
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	43.6 Å
skewness	0.245
kurtosis	-0.576
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	54020000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.937

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	Trace amine-associated receptor 12707.TAAR348
formula_weight	39076.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R
atom_count	9818

MSSHANTTSPACGLTFYDFNCSRASVTSSSERAQVMSLLLSISAITIAGNLLTITSILYFRQLQTRTNVLTLSLAVADLLVGLLIMPFSVMRSVHNCWFYGRVFCRVHTWLDYTFCTSSIVHLSCISFDRYVAISDPLRYEQRVTRRACVRMLVCCWLCLLVYGLAFMMEWNLVGLEEEVAHICPDDCPVLLNLPFAMANTIFACIVPMMLMTLAYGRIYQLARQQARKITSAAVGSNADSARSSLRREHSATITMGIIVGVFISLWIPYFVVSVTEPIFGYHASSVTWEVINWFTYINSTANPILFAAFNRPFRNAFYLILSGRMFASSCRGVDLFDVLRALAKARG

Source

organism	Petromyzon marinus
common_name	sea lamprey
ncbi_taxonomy_id	7757
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
formula_weight	28304.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MGSTVSAEDKAAAERSKMIDKNLREDGEKAAAATHRLLLLGADNSGKSTIVKQMRIYHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYELL

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	37416.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
formula_weight	7861.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	Nb35
formula_weight	15271.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHHEPEA

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia

Entity 6 polymer

description	scFv16
formula_weight	27784.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKAAAHHHHHHHH

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Spodoptera frugiperda

Entity 7 non-polymer

description	SPERMINE
formula_weight	202.3 kDa
src_method	syn
entity_count	1

▶

6. Citations (1)

▶

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.82 Å
resolution_method	—
num_particles	269228

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

Cryo-EM structure of the spermine-bound sea lamprey TAAR348-Gs complex

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Symmetry

EM 3D

5. Entities & Polymer Info (7)

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 polymer

Polymer

Source

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)