SAXSdb — 9ria

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1. Structure Basics

entry_id	9ria
deposition_date	2025-06-11
title	Cryo-EM structure of tomato NRC3-AVRcap1b complex
keywords	Effector, NLR, Plant Immunity, Resistosome, IMMUNE SYSTEM; IMMUNE SYSTEM
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	48.88 Å
rg_electron	48.59 Å
i0	1715040000.00
molecular_weight	351270.0 kDa
excluded_volume	442790 Å³
envelope_volume	636210 Å³
shell_volume	105560 Å³
envelope_diameter	176.2 Å
shell_rg	55.04 Å
envelope_rg	48.16 Å
shape_rg	48.60 Å
total_rg	48.78 Å
total_atoms	24721
n_residues	3075
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	161.5 Å
rg_real	48.71 Å
rg_real_error	1.34 Å
i0_real	1.7150e+09
i0_real_error	2.8360e+07
rg_reciprocal	48.88 Å
i0_reciprocal	1715000000.0000
total_estimate	0.8630
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.5 Å
skewness	0.308
kurtosis	-0.185
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	248500000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.763

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	NRC3
formula_weight	104764.0 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	24721

MADVAVKFELENETQLEIDNADLILGIQGEVENLLTDLNYFNAFLKEAAKSRRENEVLKELVKKIRKVVNDAEDSIDKFVVEAKRHDDKNKFAQWFHITHVARAKGVADEIKSIRERVKEIRDNDAYGLQAITLDDNFNRGDEERKAPVVEEDDVVGFDDEAKTVIDRLIGGSDYVEVVPVVGMPGLGKTTLAYKIYKDPKVEYEFFTRVWVYVSQTFKRREIFLNIISKFTRNTKQYDDTPEDDLANEVKELLGKGGKYLIVLDDVWTMEAWDRIKIAFPNNGKRNRVLMTTRQSNVAKRCNDKPHDLKFLTKDESWELLEKKVFHKEKCPPELELPGISIAEKCMGLPLAIVVIAGALIGKGKTTREWELVAASVGEHLINRDPENCKKLVQMSYDRLPYDLKACFLYCGAFPGGSQIPAKKLIRLWIAEGFIQYQGPLALEDVAEDHLNDLVNRNLVMVTQRSCSGQIKTCRVHDMLHEFCRHEAMMEENLFQEIKQGQERSFPGKQELATYRRLCIQSLIPEFLSMKPSGEHVRSFLCVGSKKIDMPPNEIPSIPKAFPLLRVLDAESIKFSRFSREFFKLFHLRYIALSTDKIKTIPADFGNLWNIQTLIVETQQATLDIKADIWNMTRLRHVCTNASATLPSTKRPKSSKDNLVNRCLQTLSTIAPECCTAEVFTRTPNLKKLGVRGKIDALLESSKDGSGSGLFSNIGKLGCLEYLKLVNDTRLSSKPLHLPPAYIFPQKLKKLSLVDTWFEWKDMSILGLLPELEVLKLKENAFKGQSWEQEDGGFPRLQVLWIERTDLTSWKASSGNFPRLKHLALISCDKLEELPAELADVKNLQLIELQSSSESAARSARAILKRNQEKEQDGDKGTGFKLSIFPHDLGLSDYKDHDGDYKDHDLDAAAADYKDDDDK

Source

organism	Solanum lycopersicum
common_name	tomato
ncbi_taxonomy_id	4081
host_organism	Nicotiana benthamiana

Entity 2 polymer

description	RxLR effector protein PITG_16705
formula_weight	78138.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MAPSIVENIKALVKSSAVTPAKLQQWLDERLEAGLVFKNMNLDEPNIFSLLHEPNFAKWVQYADDLSAKSSHKESSVISTLTSLHGDKVVYDTIQAAKLYPQLSELALKLEKDQIRFWIATRKDPSVVFEALNLNWAGISIFPKPEFSAWLKYVDDVNARHPKEAPLSIIPTLKQRFSRGDEAGTDVLLKLIANGKATTEAKTVANKVESALFDFWLNSRETPDKVMDAFKYGTTTQAFLGSPRWKEWERYLSAYNARYPEKKATAIETLTRKYGDAQLLDTLIGASSKGETKTLAAKLQAQQFDRWMNLKESPLDVYNRLRSSYGDTAFFNEPQLNVWVSYMNVFVDKNPSKVDKMFLELGDTFGDMRLFRVLGEAKKFPNLESTATKLQMEKASTLFASGKSPEGIFKVLALDNVGDDILSNTLFHKWLAYLQKFNKEHPNNQESWFDMLRISYQPFGVERIIETGRKNPLTRLMAEKVENAYHNYWLDIKMEPKTAFRSLHLDESGEKLLADPKFNTWVQYLKTFNDRYPNEKTTVIDGLRDNSHDIALLRMFSAAKNDPSTEKLATDLQSALILKWQDAKKTPEELKRVFVGVPAADEMLDRYIKLLAVASSTPYSYPYDVPDYAGYPYDVPDYAGLYPYDVPDYATRAAYPYDVPDYAGYPYDVPDYAGLYPYDVPDYA

Source

organism	Phytophthora infestans
common_name	potato late blight agent
ncbi_taxonomy_id	4787
host_organism	Nicotiana benthamiana

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	3

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6. Citations (2)

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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	3.20 Å
resolution_method	—
num_particles	267047

fit	/app/data/saxs_computation/ri/9ria/9ria.fit
pddf	/app/data/pr_computation/ri/9ria/9ria.pr.out
profile	/app/data/saxs_computation/ri/9ria/9ria.dat

Cryo-EM structure of tomato NRC3-AVRcap1b complex

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)