SAXSdb — 9y7h

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1. Structure Basics

entry_id	9y7h
deposition_date	2025-09-10
title	Gb1g2 crosslinked to PLCb3
keywords	heterotrimeric G protein, phospholipase, lipase, calcium signaling, 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	34.40 Å
rg_electron	33.70 Å
i0	252871000.00
molecular_weight	126850.0 kDa
excluded_volume	158500 Å³
envelope_volume	209950 Å³
shell_volume	51326 Å³
envelope_diameter	113.9 Å
shell_rg	40.94 Å
envelope_rg	33.34 Å
shape_rg	33.68 Å
total_rg	34.30 Å
total_atoms	17710
n_residues	1125
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	110.5 Å
rg_real	34.33 Å
rg_real_error	0.58 Å
i0_real	2.5290e+08
i0_real_error	4.0010e+06
rg_reciprocal	34.38 Å
i0_reciprocal	252900000.0000
total_estimate	0.8939
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.9 Å
skewness	0.264
kurtosis	-0.440
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0001
highest_alpha	74420000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.882

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
formula_weight	99653.9 kDa
ec_number	3.1.4.11
mutation	E60C, C193S, C221S, C358S, C516S, C824S, C834S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	17710

MAHHHHHHGTALQLEPPTVVETLRRGSKFIKWDEETSSRNLVTLRVDPNGFFLYWTGPNMCVDTLDISSIRDTRTGRYARLPKDPKIREVLGFGGPDARLEEKLMTVVSGPDPVNTVFLNFMAVQDDTAKVWSEELFKLAMNILAQNASRNTFLRKAYTKLKLQVNQDGRIPVKNILKMFSADKKRVETALESSGLKFNRSESIRPDEFSLEIFERFLNKLSLRPDIDKILLEIGAKGKPYLTLEQLMDFINQKQRDPRLNEVLYPPLRPSQARLLIEKYEPNQQFLERDQMSMEGFSRYLGGEENGILPLEALDLSTDMTQPLSAYFINSSHNTYLTAGQLAGTSSVEMYRQALLWGSRCVELDVWKGRPPEEEPFITHGFTMTTEVPLRDVLEAIAETAFKTSPYPVILSFENHVDSAKQQAKMAEYCRSIFGDALLIEPLDKYPLAPGVPLPSPQDLMGRILVKNKKRHRPSAGGPDSAGRKRPLEQSNSALSESSAATEPSSPQLGSPSSDSCPGLSNGEEVGLEKPSLEPQKSLGDEGLNRGPYVLGPADREDEEEDEEEEEQTDPKKPTTDEGTASSEVNATEEMSTLVNYIEPVKFKSFEAARKRNKCFEMSSFVETKAMEQLTKSPMEFVEYNKQQLSRIYPKGTRVDSSNYMPQLFWNVGCQLVALNFQTLDVAMQLNAGVFEYNGRSGYLLKPEFMRRPDKSFDPFTEVIVDGIVANALRVKVISGQFLSDRKVGIYVEVDMFGLPVDTRRKYRTRTSQGNSFNPVWDEEPFDFPKVVLPTLASLRIAAFEEGGKFVGHRILPVSAIRSGYHYVSLRNEANQPLSLPALLIYTEASDYIPDDHQDYAEALINPIKHVSLMDQRARQLAALIGE

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	36485.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

RQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIW

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Trichoplusia ni

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	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Trichoplusia ni

Entity 4 non-polymer

description	1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)
formula_weight	220.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CALCIUM ION
formula_weight	40.1 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	—

resolution	4.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.40 Å
resolution_method	—
num_particles	92777

fit	/app/data/saxs_computation/y7/9y7h/9y7h.fit
pddf	/app/data/pr_computation/y7/9y7h/9y7h.pr.out
profile	/app/data/saxs_computation/y7/9y7h/9y7h.dat

Gb1g2 crosslinked to PLCb3

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

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)