SAXSdb — 9vjf

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1. Structure Basics

entry_id	9vjf
deposition_date	2025-06-19
title	Cryo-EM structure of 5-HT1AR-Gi3 in complex with buspirone
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	36.28 Å
rg_electron	36.16 Å
i0	233969000.00
molecular_weight	125600.0 kDa
excluded_volume	157850 Å³
envelope_volume	196040 Å³
shell_volume	45773 Å³
envelope_diameter	120.7 Å
shell_rg	41.60 Å
envelope_rg	36.34 Å
shape_rg	36.14 Å
total_rg	36.58 Å
total_atoms	8819
n_residues	1124
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	117.0 Å
rg_real	36.21 Å
rg_real_error	0.82 Å
i0_real	2.3400e+08
i0_real_error	3.8940e+06
rg_reciprocal	36.26 Å
i0_reciprocal	234000000.0000
total_estimate	0.9002
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	47.9 Å
skewness	0.192
kurtosis	-0.595
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0001
highest_alpha	32850000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.900

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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(i) subunit alpha-3
formula_weight	40584.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	8819

MGCTLSAEDKAAVERSKMIDRNLREDGEKAAKEVKLLLLGAGESGKNTIVKQMKIIHEDGYSEDECKQYKVVVYSNTIQSIIAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMTPELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDRISQSNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHASMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRSPLTICYPEYTGSNTYEEAAAYIQCQFEDLNRRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKECGLY

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	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	2

Entity 7 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

Entity 8 non-polymer

description	Buspirone
formula_weight	385.5 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	2.70 Å
resolution_method	—
num_particles	120290

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

Cryo-EM structure of 5-HT1AR-Gi3 in complex with buspirone

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)