SAXSdb — 9vcl

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1. Structure Basics

entry_id	9vcl
deposition_date	2025-06-06
last_revision	2025-07-16
title	Cryo-EM structure of SARS-CoV-2 nsp10/nsp14:RNA:ATMP complex
keywords	SARS-CoV-2, exonuclease, nsp14, nucleotide analogue, VIRAL PROTEIN/RNA, VIRAL PROTEIN-RNA complex; VIRAL 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	38.05 Å
rg_electron	37.44 Å
i0	165382000.00
molecular_weight	90027.0 kDa
excluded_volume	106580 Å³
envelope_volume	149510 Å³
shell_volume	36477 Å³
envelope_diameter	139.5 Å
shell_rg	39.10 Å
envelope_rg	37.98 Å
shape_rg	37.34 Å
total_rg	37.78 Å
total_atoms	6217
n_residues	697
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	133.7 Å
rg_real	38.44 Å
rg_real_error	2.20 Å
i0_real	1.6540e+08
i0_real_error	3.6640e+06
rg_reciprocal	38.20 Å
i0_reciprocal	165300000.0000
total_estimate	0.8472
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.0 Å
skewness	0.497
kurtosis	-0.287
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	8226000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.793; Smooth: 0.843

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Non-structural protein 10
formula_weight	14802.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6220

AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 polymer

description	Guanine-N7 methyltransferase nsp14
formula_weight	59887.5 kDa
ec_number	2.1.1.56,3.1.13.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 3 polymer

description	RNA (26-MER)
formula_weight	8217.9 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	P

UUCUCCUAAGAAGCUAUUAAAAUCAC

Entity 4 polymer

description	RNA (28-MER)
formula_weight	8967.3 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	T

AAGUGAUUUUAAUAGCUUCUUAGGAUGA

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	;[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate ;
formula_weight	379.2 kDa
src_method	nat
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
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	3.08 Å
resolution_method	—
num_particles	71299

fit	/app/data/saxs_computation/vc/9vcl/9vcl.fit
pddf	/app/data/pr_computation/vc/9vcl/9vcl.pr.out
profile	/app/data/saxs_computation/vc/9vcl/9vcl.dat

Cryo-EM structure of SARS-CoV-2 nsp10/nsp14:RNA:ATMP complex

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)