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9xzf

hPNPase RNA loading state with extended RNA in the bottom

Method: ELECTRON MICROSCOPY D_max: 104.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xzf
deposition_date	2025-08-27
title	hPNPase RNA loading state with extended RNA in the bottom
keywords	;RNase, Protein-RNA Complex, RNA degradation, mitochondria, phosphorolytic enzyme, TRANSFERASE-RNA complex, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex ;; RNA BINDING PROTEIN/RNA
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	36.69 Å
rg_electron	35.99 Å
i0	648790000.00
molecular_weight	207410.0 kDa
excluded_volume	260090 Å³
envelope_volume	338750 Å³
shell_volume	73560 Å³
envelope_diameter	104.8 Å
shell_rg	45.85 Å
envelope_rg	35.20 Å
shape_rg	35.99 Å
total_rg	36.61 Å
total_atoms	14555
n_residues	1880
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	104.6 Å
rg_real	36.35 Å
rg_real_error	0.36 Å
i0_real	6.4880e+08
i0_real_error	7.9220e+06
rg_reciprocal	36.56 Å
i0_reciprocal	648900000.0000
total_estimate	0.9025
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	48.7 Å
skewness	-0.025
kurtosis	-0.640
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	204000000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.867

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Polyribonucleotide nucleotidyltransferase 1, mitochondrial
formula_weight	84417.1 kDa
ec_number	2.7.7.8
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	14555

MAVAVDLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPSQFMPLVVDYRQKAAAAGRIPTNYLRREIGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKYTHKLAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPEADPYEIIESFNVVAKEVFRSIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIPRDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDEETFSVFAPTPSAMHEARDFITEICKDDQEQQLEFGAVYTATITEIRDTGVMVKLYPNMTAVLLHNTQLDQRKIKHPTALGLEVGQEIQVKYFGRDPADGRMRLSRKVLQSPATTVVRTLNDRSSIVMGEPISQSSSNSQSGSGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	RNA (31-MER)
formula_weight	9825.1 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	D

ACACAACACAACACACACCACACACACAUAA

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 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	—

resolution	2.650 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.65 Å
resolution_method	—
num_particles	89314

fit	/app/data/saxs_computation/xz/9xzf/9xzf.fit
pddf	/app/data/pr_computation/xz/9xzf/9xzf.pr.out
profile	/app/data/saxs_computation/xz/9xzf/9xzf.dat

hPNPase RNA loading state with extended RNA in the bottom

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

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)