SAXSdb — 9upc

▼

1. Structure Basics

entry_id	9upc
deposition_date	2025-04-28
title	Structure of human TREX-2
keywords	mRNA nuclear export, TREX-2, UAP56, gene regulation; GENE REGULATION
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	31.78 Å
rg_electron	30.81 Å
i0	119730000.00
molecular_weight	87434.0 kDa
excluded_volume	109580 Å³
envelope_volume	135120 Å³
shell_volume	36730 Å³
envelope_diameter	100.8 Å
shell_rg	37.66 Å
envelope_rg	30.78 Å
shape_rg	30.81 Å
total_rg	31.39 Å
total_atoms	6143
n_residues	759
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

▼

3. P(r) Analysis (GNOM)

dmax	101.0 Å
rg_real	31.71 Å
rg_real_error	0.70 Å
i0_real	1.1970e+08
i0_real_error	2.0050e+06
rg_reciprocal	31.74 Å
i0_reciprocal	119700000.0000
total_estimate	0.9074
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	38.4 Å
skewness	0.188
kurtosis	-0.655
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	29130000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.946

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Germinal-center associated nuclear protein
formula_weight	51891.7 kDa
ec_number	2.3.1.48,2.3.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6159

SAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGGGSDEVDAAAEGSEGLGPCVLSLSTLIGTVAETSKEKYRLLDQRDRIMRQARVKRTDLDKARTFVGTCLDMCPEKERYMRETRSQLSVFEVVPGTDQVDHAAAVKEYSRSSADQEEPLPHELRPLPVLSRTMDYLVTQIMDQKEGSLRDWYDFVWNRTRGIRKDITQQHLCDPLTVSLIEKCTRFHIHCAHFMCEEPMSSFDAKINNENMTKCLQSLKEMYQDLRNKGVFCASEAEFQGYNVLLSLNKGDILREVQQFHPAVRNSSEVKFAVQAFAALNSNNFVRFFKLVQSASYLNACLLHCYFSQIRKDALRALNFAYTVSTQRSTIFPLDGVVRMLLFRDCEEATDFLTCHGLTVSDGCVELNRSAFLEPEGLSKTRKSVFITRKLTVSVGEIVNGGPLPPVPRHTPVCSFNSQNKYIGESLAAELPV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	PCI domain-containing protein 2
formula_weight	49171.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

DYKDHDGDYKDHDIDYKDDDDKGSAAAMAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDEMFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFANNADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFKIYFKINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	26S proteasome complex subunit SEM1
formula_weight	8284.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAELEKHGYKMETS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

▶

6. Citations (1)

▶

resolution	3.14 Å
resolution_method	—
num_particles	108904

fit	/app/data/saxs_computation/up/9upc/9upc.fit
pddf	/app/data/pr_computation/up/9upc/9upc.pr.out
profile	/app/data/saxs_computation/up/9upc/9upc.dat

Structure of human TREX-2

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

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)