SAXSdb — 9vj5

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1. Structure Basics

entry_id	9vj5
deposition_date	2025-06-19
title	Cryo-EM structure of 5-HT1AR-GoA in complex with gepirone
keywords	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	36.43 Å
rg_electron	36.24 Å
i0	449971000.00
molecular_weight	115230.0 kDa
excluded_volume	111560 Å³
envelope_volume	193590 Å³
shell_volume	45290 Å³
envelope_diameter	120.6 Å
shell_rg	41.48 Å
envelope_rg	36.23 Å
shape_rg	36.24 Å
total_rg	36.48 Å
total_atoms	8709
n_residues	1113
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	117.1 Å
rg_real	36.36 Å
rg_real_error	0.78 Å
i0_real	4.5000e+08
i0_real_error	6.9260e+06
rg_reciprocal	36.41 Å
i0_reciprocal	450000000.0000
total_estimate	0.9011
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	49.0 Å
skewness	0.170
kurtosis	-0.646
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	35420000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.919

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Guanine nucleotide-binding protein G(o) subunit alpha
formula_weight	40081.4 kDa
ec_number	3.6.5.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	8709

MGSTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGAGESGKNTIVKQMKIIHEDGFSGEDVKQYKPVVYSNTIQSLAAIVRAMDTLGIEYGDKERKADAKMVCDVVSRMEDTEPFSAELLSAMMRLWGDSGIQECFNRSREYQLNDSAKYYLDSLDRIGAADYQPTEQDILRTRVKTTGIVETHFTFKNLHFRLFDVGAQRSERKKWIHCFEDVTAIIFCVALSGYDQVLHEDETTNRMHASLKLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDAAAYIQAQFESKNRSPNKEIYCHMTCSTDTNNIQVVFDAVTDIIIANNLRGCGLY

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(T) subunit beta-1
formula_weight	39418.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

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	7861.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	scFv16
formula_weight	26679.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKAAA

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	Soluble cytochrome b562,5-hydroxytryptamine receptor 1A
formula_weight	60921.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

DYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTTMADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGSTLEVLFQGPTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCCTSSIWHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPEDRSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCRQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 6 non-polymer

description	Gepirone
formula_weight	359.5 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	;(2R)-1-(heptadecanoyloxy)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate ;
formula_weight	953.1 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	triclinic

resolution	2.69 Å
resolution_method	—
num_particles	180175

fit	/app/data/saxs_computation/vj/9vj5/9vj5.fit
pddf	/app/data/pr_computation/vj/9vj5/9vj5.pr.out
profile	/app/data/saxs_computation/vj/9vj5/9vj5.dat

Cryo-EM structure of 5-HT1AR-GoA in complex with gepirone

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 (8)

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

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)