SAXSdb — 9w0m

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1. Structure Basics

entry_id	9w0m
deposition_date	2025-07-24
title	Cryo-EM structure of S1P2 in complex with heterotrimeric G protein
keywords	;G protein-coupled receptor, Bitter taste receptor 14, Bitter taste receptor 46, ligand binding, signal transduction, MEMBRANE PROTEIN ;; MEMBRANE 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	35.19 Å
rg_electron	35.24 Å
i0	146177000.00
molecular_weight	98028.0 kDa
excluded_volume	123230 Å³
envelope_volume	167660 Å³
shell_volume	41058 Å³
envelope_diameter	125.8 Å
shell_rg	39.89 Å
envelope_rg	35.39 Å
shape_rg	35.25 Å
total_rg	35.55 Å
total_atoms	6881
n_residues	888
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	121.3 Å
rg_real	35.37 Å
rg_real_error	0.97 Å
i0_real	1.4620e+08
i0_real_error	2.5730e+06
rg_reciprocal	35.26 Å
i0_reciprocal	146200000.0000
total_estimate	0.8558
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.0 Å
skewness	0.468
kurtosis	-0.305
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	37490000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.897; Smooth: 0.779

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Sphingosine 1-phosphate receptor 2
formula_weight	44592.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6881

MKTIIALSYIFCLVFAMGSLYSEYLNPNKVQEHYNYTKETLETQETTSRQVASAFIVILCCAIVVENLLVLIAVARNSKFHSAMYLFLGNLAASDLLAGVAFVANTLLSGSVTLRLTPVQWFAREGSAFITLSASVFSLLAIAIERHVAIAKVKLYGSDKSCRMLLLIGASWLISLVLGGLPILGWNCLGHLEACSTVLPLYAKHYVLCVVTIFSIILLAIVALYVRIYCVVRSSHADMAAPQTLALLKTVTIVLGVFIVCWLPAFSILLLDYACPVHSCPILYKAHYFFAVSTLNSLLNPVIYTWRSRDLRREVLRPLQCWRPGVGVQGRRRGGTPGHHLLPLRSSSSLERGMHMPTSPTFLEGNTVVWSHPQFEKGGGSGGGSGGSAWSHPQFEKDYKDDDDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
formula_weight	6000.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

IAQARKLVQQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASQNPFR

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(T) subunit beta-1
formula_weight	38745.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MHHHHHHGSLLQSELDELRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTRQGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPDGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

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) subunit alpha-1
formula_weight	40447.1 kDa
mutation	S47C/G202T/G203A/E245A/A326S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKCTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVTAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

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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	3.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.80 Å
resolution_method	—
num_particles	415313

fit	/app/data/saxs_computation/w0/9w0m/9w0m.fit
pddf	/app/data/pr_computation/w0/9w0m/9w0m.pr.out
profile	/app/data/saxs_computation/w0/9w0m/9w0m.dat

Cryo-EM structure of S1P2 in complex with heterotrimeric G protein

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)