SAXSdb — 9yda

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1. Structure Basics

entry_id	9yda
deposition_date	2025-09-22
title	Cryo-EM structure of active human green cone opsin in complex with chimeric G protein (miniGist)
keywords	G protein-coupled receptor, cone opsin, SIGNALING PROTEIN; SIGNALING 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	39.22 Å
rg_electron	39.10 Å
i0	247498000.00
molecular_weight	128460.0 kDa
excluded_volume	161120 Å³
envelope_volume	223960 Å³
shell_volume	49178 Å³
envelope_diameter	130.2 Å
shell_rg	43.02 Å
envelope_rg	38.78 Å
shape_rg	39.11 Å
total_rg	39.30 Å
total_atoms	9036
n_residues	1149
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	128.4 Å
rg_real	39.15 Å
rg_real_error	1.07 Å
i0_real	2.4750e+08
i0_real_error	4.2640e+06
rg_reciprocal	39.20 Å
i0_reciprocal	247500000.0000
total_estimate	0.9002
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	51.4 Å
skewness	0.184
kurtosis	-0.647
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	44860000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.947

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Medium-wave-sensitive opsin 1
formula_weight	40700.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R
atom_count	9036

MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVTETSQVAPA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Chlorocebus aethiops

Entity 2 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	38878.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGSSGTETSQVAPA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Chlorocebus aethiops

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	G

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Chlorocebus aethiops

Entity 4 polymer

description	scFv16
formula_weight	27784.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKAAAHHHHHHHH

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	Genome polyprotein,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
formula_weight	57380.7 kDa
ec_number	3.6.5.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MLQNELALKLAGLDINKTGGSGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFGYGLQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKGSGSGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDVTDIIILEDLKSCGLF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Chlorocebus aethiops

Entity 6 non-polymer

description	RETINAL
formula_weight	284.4 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	2.90 Å
resolution_method	—
num_particles	639873

fit	/app/data/saxs_computation/yd/9yda/9yda.fit
pddf	/app/data/pr_computation/yd/9yda/9yda.pr.out
profile	/app/data/saxs_computation/yd/9yda/9yda.dat

Cryo-EM structure of active human green cone opsin in complex with chimeric G protein (miniGist)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (6)

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

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)