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9xf9

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with WXS

Method: X-RAY DIFFRACTION D_max: 124.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xf9
deposition_date	2025-10-28
last_revision	2026-05-06
title	Crystal structure of Kasokero virus cap- snatching endonuclease in complex with WXS
keywords	cap-snatching endonuclease, inhibitor, HYDROLASE; HYDROLASE
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	36.04 Å
rg_electron	36.58 Å
i0	169259000.00
molecular_weight	69787.0 kDa
excluded_volume	67414 Å³
envelope_volume	123190 Å³
shell_volume	31775 Å³
envelope_diameter	131.2 Å
shell_rg	37.77 Å
envelope_rg	36.54 Å
shape_rg	36.57 Å
total_rg	36.65 Å
total_atoms	5280
n_residues	677
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	124.2 Å
rg_real	36.61 Å
rg_real_error	1.23 Å
i0_real	1.6930e+08
i0_real_error	2.8350e+06
rg_reciprocal	36.26 Å
i0_reciprocal	169200000.0000
total_estimate	0.7546
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.1 Å
skewness	0.640
kurtosis	-0.258
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	7558000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.648; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.506; Smooth: 0.355

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	RNA-directed RNA polymerase L
formula_weight	34355.0 kDa
ec_number	2.7.7.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5892

GPLGSKKPIALICAELYKPFQDLFAALPKDCSEECQTLFEDIRNSESHASAWSSALRIKGVAYEGFFSLTNSWRYIPEDLKPTLGMAIQTVFPDKFEKFLERTHLHPEYRDFTPDYLMCRSRIFKSDRLNRSNVAVSRGKDKGGKKKETTVNKDQDDDAQSAVLLSHKKRFPMPEIAVQEVSSVSAVVDRFKSKSSEKGRPIRQEESRPKTESMQEDIEVDELLIVEVGYQTDIEGKVISDIEKWKGVVNLMSHLGIKVNVLTCADNSQTPRTDWWIDEKYVRLLLNSISYLFKELLENS

Source

organism	Kasokero virus
ncbi_taxonomy_id	1712570
host_organism	Trichoplusia ni

Entity 2 polymer

description	mAb 2E9 Fab heavy chain
formula_weight	24722.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EVKLEESGGGLVRPGGSRKLSCAASGFTFSSYGMQWVRQAPEKGLEWVAYISSGSRTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYYCATGYGGTWFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	mAb 2E9 Fab light chain
formula_weight	23971.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

QIVLSQSPLSLPVSLGDQASISCRSSQSLLHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 4 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	nat
entity_count	2

Entity 5 non-polymer

description	Cap-dependent endonuclease-IN-27
formula_weight	439.4 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	612

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6. Citations (1)

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length_a	37.320 Å
length_b	80.600 Å
length_c	116.140 Å
angle_alpha	90.00 °
angle_beta	93.19 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.850 Å
resolution_low	28.990 Å
r_factor	0.1804
r_work	0.1786
r_free	0.2143

fit	/app/data/saxs_computation/xf/9xf9/9xf9.fit
pddf	/app/data/pr_computation/xf/9xf9/9xf9.pr.out
profile	/app/data/saxs_computation/xf/9xf9/9xf9.dat

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with WXS

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)