Human Brain RNA Vault Shoulder bound to ADPR, focused refinement (EMPIAR-10766)

Method: ELECTRON MICROSCOPY D_max: 110.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	11dr
deposition_date	2026-02-18
title	Human Brain RNA Vault Shoulder bound to ADPR, focused refinement (EMPIAR-10766)
keywords	RNA Vault, ADPR, ADP-ribose, Nucleotide, Major Vault Protein, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	31.25 Å
rg_electron	30.57 Å
i0	125888000.00
molecular_weight	86843.0 kDa
excluded_volume	107890 Å³
envelope_volume	134960 Å³
shell_volume	37036 Å³
envelope_diameter	118.7 Å
shell_rg	37.36 Å
envelope_rg	30.89 Å
shape_rg	30.55 Å
total_rg	31.24 Å
total_atoms	12176
n_residues	762
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	110.1 Å
rg_real	31.25 Å
rg_real_error	0.97 Å
i0_real	1.2590e+08
i0_real_error	1.9260e+06
rg_reciprocal	31.26 Å
i0_reciprocal	125900000.0000
total_estimate	0.8633
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.5 Å
skewness	0.331
kurtosis	-0.390
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	36310000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; Smooth: 0.942

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Major vault protein
formula_weight	99452.8 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	12176

MATEEFIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPMRMVTVPPRHYCTVANPVSRDAQGLVLFDVTGQVRLRHADLEIRLAQDPFPLYPGEVLEKDITPLQVVLPNTALHLKALLDFEDKDGDKVVAGDEWLFEGPGTYIPRKEVEVVEIIQATIIRQNQALRLRARKECWDRDGKERVTGEEWLVTTVGAYLPAVFEEVLDLVDAVILTEKTALHLRARRNFRDFRGVSRRTGEEWLVTVQDTEAHVPDVHEEVLGVVPITTLGPHNYCVILDPVGPDGKNQLGQKRVVKGEKSFFLQPGEQLEQGIQDVYVLSEQQGLLLRALQPLEEGEDEEKVSHQAGDHWLIRGPLEYVPSAKVEVVEERQAIPLDENEGIYVQDVKTGKVRAVIGSTYMLTQDEVLWEKELPPGVEELLNKGQDPLADRGEKDTAKSLQPLAPRNKTRVVSYRVPHNAAVQVYDYREKRARVVFGPELVSLGPEEQFTVLSLSAGRPKRPHARRALCLLLGPDFFTDVITIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIASRVRGAVASVTFDDFHKNSARIIRTAVFGFETSEAKGPDGMALPRPRDQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEALSMAVESTGTAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELQRVQKVRELELVYARAQLELEVSKAQQLAEVEVKKFKQMTEAIGPSTIRDLAVAGPEMQVKLLQSLGLKSTLITDGSTPINLFNTAFGLLGMGPEGQPLGRRVASGPSPGEGISPQSAQAPQAPGDNHVVPVLR

Entity 2 non-polymer

description	;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ;
formula_weight	559.3 kDa
src_method	syn
entity_count	3

▶

6. Citations (1)

▶

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	2.62 Å
resolution_method	—
num_particles	464690

fit	/app/data/saxs_computation/1d/11dr/11dr.fit
pddf	/app/data/pr_computation/1d/11dr/11dr.pr.out
profile	/app/data/saxs_computation/1d/11dr/11dr.dat

Human Brain RNA Vault Shoulder bound to ADPR, focused refinement (EMPIAR-10766)

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 (2)

Entity 1 polymer

Polymer

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)