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9qww

Cryo-EM structure of plant resistance protein NRC2 dimer bound to nematode effector SPRYSEC-15

Method: ELECTRON MICROSCOPY D_max: 153.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qww
deposition_date	2025-04-15
title	Cryo-EM structure of plant resistance protein NRC2 dimer bound to nematode effector SPRYSEC-15
keywords	Helper resistance protein, Plant immunity, Suppressor, PLANT PROTEIN; PLANT 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	45.68 Å
rg_electron	45.49 Å
i0	588040000.00
molecular_weight	204390.0 kDa
excluded_volume	257680 Å³
envelope_volume	341020 Å³
shell_volume	63739 Å³
envelope_diameter	149.4 Å
shell_rg	48.25 Å
envelope_rg	45.53 Å
shape_rg	45.51 Å
total_rg	45.54 Å
total_atoms	14400
n_residues	1834
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	153.1 Å
rg_real	45.82 Å
rg_real_error	1.46 Å
i0_real	5.8800e+08
i0_real_error	1.0850e+07
rg_reciprocal	45.69 Å
i0_reciprocal	587900000.0000
total_estimate	0.8690
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	48.1 Å
skewness	0.345
kurtosis	-0.563
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	65500000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.728

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	NRC2a
formula_weight	101270.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	14400

MANVAVEFLVQNLMQLLRDNAELIVGVKDSAESLLQDLNDFNAFLKQTAKSRTENDVHKELVKKIKTVVNSAEDAIDKFVIEAKLHKDKGVGRFVDVKHYKRVYDVAGEIKTIRDKVKEIRLNNALDLQALQDEDQSAKGVQERKPPVVEEDDVVGFEEEADKVINRLLGGSSGLEVVPVVGMPGLGKTTLANKIYKHPDIGYQFFTRIWVYVSQSYRRRELFLNIISKFTRNTKQYHDMCEEDLADEIEDFLGKGGKYLIVLDDVWSPDAWERIRIAFPNNNKSNRILLTTRDSKVAKQCKQCIGIPHDLKFLTEDESWILLEKKVFHKDKCPPELELSGKSIAKKCNGLPLAIVVIAGALIGKGKTSREWKQVDESVGEHLINKDQPENCNKLVQLSYDRLSYDLKACFLYCGAFPGGFEIPAWKLIRLWIAEGFIQYKGHLSLECKAEDNLNDLINRNLVMVMQRTSDGQIKTCRLHDMLHEFCRQEAMKEENLFQEIKLGAEQYFPGKRELATYRRLCIHSSVLEFISTKPSGEHVRSFLSFSLKKIEMPSVDIPTIPKGFPLLRVFDVESINFSRFSKEFFQLYHLRYIAFSSDTIKIIPKHIGELWNIQTLIINTQQRSLDIQANIWNMERLRHLHTNSSAKLPVPVTPRSSKVPLVNQSLQTLSTIAPESCTEEVFARTPNLKKLGIRGKIAVLLEPNKSLLKNVKKLESLENLKLINDSSQTGKGLRLPPSYIFPTKLRKLSLVDTWLEWNDMSILGQMEHLEVLKLKENGFMGECWESVGGFCSLLVLWIERTDLVSWKASADHFPRLKHLVLICCDKLKEIPIGLADIRSFQVMELQNSTKTAAISARGIRDKKDKQTQEGTNNNGFKLSIFPPDL

Source

organism	Nicotiana benthamiana
ncbi_taxonomy_id	4100
host_organism	Nicotiana benthamiana

Entity 2 polymer

description	Truncated secreted SPRY domain-containing protein 15
formula_weight	25402.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

GPSPKANAKLEKVPSGNAESTPVLTLQNRWAYSARDEKLAWDSAARDEKLELTEPAGLIVQFIGENSKHRSVRAKLPIPKGNSGIFYYEVTISGDGDAIYIGLATEQMPLRDTHVGYNEGTYGYGSSGKFWGHEVGGCSHWGNERPYIDGQPKFDRNNIIGCGVNLKTRQIIYTHNGRPLETTGLLVAESAAELYPCVSLFTSGNEIEANFGTKPFKFNIAEGIDDVVGFEE

Source

organism	Globodera rostochiensis
ncbi_taxonomy_id	31243
host_organism	Nicotiana benthamiana

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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	3.80 Å
resolution_method	—
num_particles	102500

fit	/app/data/saxs_computation/qw/9qww/9qww.fit
pddf	/app/data/pr_computation/qw/9qww/9qww.pr.out
profile	/app/data/saxs_computation/qw/9qww/9qww.dat

Cryo-EM structure of plant resistance protein NRC2 dimer bound to nematode effector SPRYSEC-15

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)