SAXSdb — 9u4y

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1. Structure Basics

entry_id	9u4y
deposition_date	2025-03-20
title	cryo-EM structure of Xenopus laevis GnRHR bound with mammal GnRH
keywords	Cryo-EM, GnRHR, Gonadotropin-Releasing Hormone Receptor, 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	38.08 Å
rg_electron	38.00 Å
i0	232512000.00
molecular_weight	124640.0 kDa
excluded_volume	156440 Å³
envelope_volume	206230 Å³
shell_volume	46632 Å³
envelope_diameter	126.9 Å
shell_rg	42.16 Å
envelope_rg	37.80 Å
shape_rg	38.01 Å
total_rg	38.23 Å
total_atoms	17343
n_residues	1117
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	124.7 Å
rg_real	38.04 Å
rg_real_error	1.15 Å
i0_real	2.3250e+08
i0_real_error	4.0760e+06
rg_reciprocal	38.07 Å
i0_reciprocal	232500000.0000
total_estimate	0.8991
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	47.5 Å
skewness	0.199
kurtosis	-0.643
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	36810000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.931

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	37784.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	17343

GSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

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	7861.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Gonadoliberin-1
formula_weight	1183.3 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QHWSYGLRPGX

Entity 4 polymer

description	Guanine nucleotide-binding protein G(q) subunit alpha-1
formula_weight	28084.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNLREYNLV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	scFv16
formula_weight	30363.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 6 polymer

description	Beta-2 adrenergic receptor,Gonadotropin-releasing hormone receptor
formula_weight	56891.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSDYKDDDDVHHHHHHHHDMGQPGNGSAFLLAPNGSHAPDHDVTQQRDEENLYFQGASMLTMSYQGIMDSQDLCALNRSCFHLKEQEKTYGPNITVLNDKAFILPTFSTAAKIRVAITCVLFIFSACFNIAALWTITYKYKKKSHIRILIINLVAADLFITLVVMPLDAVWNVTLQWYAGDLACRVLMFLKLAAMYSSAFVTVVISLDRQAAILNPLGIGDAKKKNKIMLCVAWFLSYLLAIPQLFVFHTVSRSEPIHFVQCATVGSFQAHWQETIYNMFTFFCLFLLPLLIMVSCYTRILMEISHKMKATCVSSKEIDLRRSSNNIPRARMRTLKMSLVIVLTFIVCWTPYYLLGIWYWFSPEMLTEEKVPPSLSHILFLFGLLNTCLDPIIYGLFTIHFRREIRRVCRCAAQGKDHDTASVGTGSFRITTTPAPIKRTVGVLGGSGKFELEVTGHGLHSGKCDQCQGRIVESFM

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
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	2.67 Å
resolution_method	—
num_particles	255764

fit	/app/data/saxs_computation/u4/9u4y/9u4y.fit
pddf	/app/data/pr_computation/u4/9u4y/9u4y.pr.out
profile	/app/data/saxs_computation/u4/9u4y/9u4y.dat

cryo-EM structure of Xenopus laevis GnRHR bound with mammal GnRH

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)