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9qwn

Human UPF1 in complex with the histone stem loop RNA

Method: ELECTRON MICROSCOPY D_max: 93.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qwn
deposition_date	2025-04-14
title	Human UPF1 in complex with the histone stem loop RNA
keywords	ATP-DEPENDENT HELICASE RENT1, UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG, HUPF1, UP FRAMESHIFT, histone stem loop mRNA, HYDROLASE; HYDROLASE
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	30.27 Å
rg_electron	29.37 Å
i0	170405000.00
molecular_weight	97800.0 kDa
excluded_volume	120080 Å³
envelope_volume	152760 Å³
shell_volume	42301 Å³
envelope_diameter	98.8 Å
shell_rg	37.45 Å
envelope_rg	29.24 Å
shape_rg	29.36 Å
total_rg	30.09 Å
total_atoms	6825
n_residues	823
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	93.5 Å
rg_real	30.12 Å
rg_real_error	0.44 Å
i0_real	1.7040e+08
i0_real_error	2.3650e+06
rg_reciprocal	30.19 Å
i0_reciprocal	170400000.0000
total_estimate	0.9036
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	36.0 Å
skewness	0.173
kurtosis	-0.498
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	26220000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Isoform 2 of Regulator of nonsense transcripts 1
formula_weight	89972.2 kDa
ec_number	3.6.4.12,3.6.4.13
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6825

TKDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVETVHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVITKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEGPLNNLRESLMQFS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli DH5[alpha]

Entity 2 polymer

description	RNA stem loop
formula_weight	11896.9 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	D

UUUUUUUUUUUUCCAAAGGCUCUUUUCAGAGCCACCCA

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

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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	3.60 Å
resolution_method	—
num_particles	300222

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

Human UPF1 in complex with the histone stem loop RNA

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

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)