SAXSdb — 9vjg

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1. Structure Basics

entry_id	9vjg
deposition_date	2025-06-19
title	Cryo-EM structure of 5-HT1AR-Gz in complex with (R)-8-OH-DPAT
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	37.16 Å
rg_electron	36.90 Å
i0	524678000.00
molecular_weight	124170.0 kDa
excluded_volume	120020 Å³
envelope_volume	214030 Å³
shell_volume	48743 Å³
envelope_diameter	124.4 Å
shell_rg	42.38 Å
envelope_rg	36.96 Å
shape_rg	36.90 Å
total_rg	37.13 Å
total_atoms	9387
n_residues	1242
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	125.5 Å
rg_real	38.37 Å
rg_real_error	0.46 Å
i0_real	5.2330e+08
i0_real_error	7.7140e+06
rg_reciprocal	37.12 Å
i0_reciprocal	524700000.0000
total_estimate	0.6956
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	52.5 Å
skewness	0.320
kurtosis	-0.264
angular_range	— – 0.2150 Å⁻¹
current_alpha	2.2030
highest_alpha	35650000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 0.890; Sysdev: 0.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.745

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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(z) subunit alpha
formula_weight	40613.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	9387

MGSTVSAEDKAAAERSKMIDKNLREDGEKQRREIKLLLLGTSNSGKNTIVKQMKIIHSGGFNLEACKEYKPLIIYNAIDSLTRIIRALAALRIDFHNPDRAYDAVQLFALTGPAESKGEITPELLGVMRRLWADPGAQACFSRSSEYHLEDNAAYYLNDLERIAAADYIPTVEDILRSRDMTTGIVENKFTFKELTFKMVDVGAQRSERKKWIHCFEGVTAIIFCVELSGYDLKLYEDNQTSRMAASLKLFDSICNNKWFIDTSLILFLNKKDLLAEKIRRIPLTICFPEYKGQNTYEEAAVYIQRQFEDLNRNKETKEIYSHFTCSTDTSNIQFVFDAVTDVIIQNNLKYIGLC

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	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	(7~{R})-7-(dipropylamino)-5,6,7,8-tetrahydronaphthalen-1-ol
formula_weight	247.4 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	2.67 Å
resolution_method	—
num_particles	105515

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

Cryo-EM structure of 5-HT1AR-Gz in complex with (R)-8-OH-DPAT

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)