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9tes

Crystal structure of beta-TrCP bound by diphosphorylated PDCD4 degron peptide

Method: X-RAY DIFFRACTION D_max: 72.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tes
deposition_date	2025-11-26
title	Crystal structure of beta-TrCP bound by diphosphorylated PDCD4 degron peptide
keywords	E3 ligase, phosphodegron, beta-TrCP, i-kappa-B-alpha, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

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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	21.84 Å
rg_electron	21.04 Å
i0	30466600.00
molecular_weight	41249.0 kDa
excluded_volume	51117 Å³
envelope_volume	59090 Å³
shell_volume	23366 Å³
envelope_diameter	74.2 Å
shell_rg	27.93 Å
envelope_rg	21.34 Å
shape_rg	21.03 Å
total_rg	21.88 Å
total_atoms	2892
n_residues	359
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	72.5 Å
rg_real	21.78 Å
rg_real_error	0.46 Å
i0_real	3.0470e+07
i0_real_error	4.2050e+05
rg_reciprocal	21.79 Å
i0_reciprocal	30470000.0000
total_estimate	0.7007
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	26.0 Å
skewness	0.308
kurtosis	-0.255
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	9905000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 0.207; Positv: 1.000; Valcen: 0.991; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	F-box/WD repeat-containing protein 1A
formula_weight	41829.7 kDa
mutation	L188E, L192E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3129

GSGMEWKKEIERMVRTDSLWRGLAERRGWGQYLFKNKPPDGNAPPNSFYRALYPKIIQDIETIESNWRCGRHSLQRIHCRSETSKGVYCLQYDDQKIVSGLRDNTIKIWDKNTLECKRILTGHTGSVLCLQYDERVIITGSSDSTVRVWDVNTGEMLNTLIHHCEAVLHLRFNNGMMVTCSKDRSIAVWDMASPTDITLRRVLVGHRAAVNVVDFDDKYIVSASGDRTIKVWNTSTCEFVRTLNGHKRGIACLQYRDRLVVSGSSDNTIRLWDIECGACLRVLEGHEELVRCIRFDNKRIVSGAYDGKIKVWDLVAALDPRAPAGTLCLRTLVEHSGRVFRLQFDEFQIVSSSHDDTILIWDFLN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Programmed cell death protein 4
formula_weight	1486.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SSRDSGRGDSVSD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	synthetic construct

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	228

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6. Citations (1)

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length_a	44.719 Å
length_b	46.971 Å
length_c	150.861 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.217 Å
resolution_low	75.430 Å
r_factor	0.2136
r_work	0.2122
r_free	0.2404

fit	/app/data/saxs_computation/te/9tes/9tes.fit
pddf	/app/data/pr_computation/te/9tes/9tes.pr.out
profile	/app/data/saxs_computation/te/9tes/9tes.dat

Crystal structure of beta-TrCP bound by diphosphorylated PDCD4 degron peptide

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

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)