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9vin

Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD

Method: ELECTRON MICROSCOPY D_max: 184.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vin
deposition_date	2025-06-18
title	Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD
keywords	TNFR1, RIPK1, TRADD, Death domain, APOPTOSIS; APOPTOSIS
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	52.54 Å
rg_electron	53.12 Å
i0	1764760000.00
molecular_weight	345090.0 kDa
excluded_volume	430730 Å³
envelope_volume	577830 Å³
shell_volume	93462 Å³
envelope_diameter	204.0 Å
shell_rg	52.62 Å
envelope_rg	53.52 Å
shape_rg	53.10 Å
total_rg	53.16 Å
total_atoms	24264
n_residues	2966
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	184.7 Å
rg_real	52.97 Å
rg_real_error	1.81 Å
i0_real	1.7650e+09
i0_real_error	3.3520e+07
rg_reciprocal	52.17 Å
i0_reciprocal	1763000000.0000
total_estimate	0.5547
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	49.2 Å
skewness	0.650
kurtosis	-0.142
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0001
highest_alpha	2113000000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.581; Stabil: 1.000; Sysdev: 0.007; Positv: 1.000; Valcen: 0.973; Smooth: 0.469

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Tumor necrosis factor receptor type 1-associated DEATH domain protein
formula_weight	13234.9 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	E,F,N,V,W
atom_count	24273

GPGSAQTFLFQGQPVVNRPLSLKDQQTFARSVGLKWRKVGRSLQRGCRALRDPALDSLAYEYEREGLYEQAFQLLRRFVQAEGRRATLQRLVEALEENELTSLAEDLLGLTDPNGGLA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Receptor-interacting serine/threonine-protein kinase 1
formula_weight	13242.9 kDa
ec_number	2.7.11.1
src_method	man
entity_count	13

Polymer

type	polypeptide(L)
strand_id	i,j,k,l,m,n,o,p,q,r,s,t,u

GPGSTNTNFKEEPAAKYQAIFDNTTSLTDKHLDPIRENLGKHWKNCARKLGFTQSQIDEIDHDYERDGLKEKVYQMLQKWVMREGIKGATVGKLAQALHQCSRIDLLSSLIYVSQN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Tumor necrosis factor receptor superfamily member 1A, membrane form
formula_weight	13334.2 kDa
src_method	man
entity_count	13

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,G,a,b,c,d,e,f,g,h

GPGSEDSAHKPQSLDTDDPATLYAVVENVPPLRWKEFVRRLGLSDHEIDRLELQNGRCLREAQYSMLATWRRRTPRREATLELLGRVLRDMDLLGCLEDIEEALCGPAALPPAPSLLR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

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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	triclinic

resolution	3.41 Å
resolution_method	—
num_particles	68510

fit	/app/data/saxs_computation/vi/9vin/9vin.fit
pddf	/app/data/pr_computation/vi/9vin/9vin.pr.out
profile	/app/data/saxs_computation/vi/9vin/9vin.dat

Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD

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 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)