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9up3

Crystal structure of Ebola virus VP30 and its peptide NPL3

Method: X-RAY DIFFRACTION D_max: 102.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9up3
deposition_date	2025-04-27
last_revision	2026-04-29
title	Crystal structure of Ebola virus VP30 and its peptide NPL3
keywords	Ebola virus, VP30, VIRAL PROTEIN; VIRAL PROTEIN
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	29.40 Å
rg_electron	29.11 Å
i0	56214300.00
molecular_weight	59989.0 kDa
excluded_volume	75818 Å³
envelope_volume	100550 Å³
shell_volume	29749 Å³
envelope_diameter	108.7 Å
shell_rg	34.97 Å
envelope_rg	29.52 Å
shape_rg	29.09 Å
total_rg	29.78 Å
total_atoms	4217
n_residues	530
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	102.1 Å
rg_real	29.49 Å
rg_real_error	0.95 Å
i0_real	5.6210e+07
i0_real_error	9.8220e+05
rg_reciprocal	29.45 Å
i0_reciprocal	56210000.0000
total_estimate	0.7889
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	28.4 Å
skewness	0.416
kurtosis	-0.343
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	27090000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Transcriptional activator VP30
formula_weight	14464.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,D,G
atom_count	4407

GPKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPCESSAVVVSGLRTLVP

Source

organism	Ebola virus
ncbi_taxonomy_id	1570291
host_organism	Escherichia coli

Entity 2 polymer

description	Peptide NPL3
formula_weight	1641.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	F,C,E,H

QRPRVEPPDPEYR

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	190

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6. Citations (1)

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length_a	47.700 Å
length_b	53.726 Å
length_c	82.876 Å
angle_alpha	72.96 °
angle_beta	81.28 °
angle_gamma	63.80 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.040 Å
resolution_low	46.600 Å
r_factor	—
r_work	0.2296
r_free	0.2573

fit	/app/data/saxs_computation/up/9up3/9up3.fit
pddf	/app/data/pr_computation/up/9up3/9up3.pr.out
profile	/app/data/saxs_computation/up/9up3/9up3.dat

Crystal structure of Ebola virus VP30 and its peptide NPL3

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)