SAXSdb — 9pz0

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1. Structure Basics

entry_id	9pz0
deposition_date	2025-08-08
last_revision	2025-09-17
title	SARS-CoV-2 core polymerase complex with two UTP incorporation
keywords	RNA-dependent RNA polymerase (RdRp), Viral RNA synthesis, Uridine triphosphate, nsp7, nsp8, nsp12, VIRAL PROTEIN; VIRAL PROTEIN
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	42.36 Å
rg_electron	41.80 Å
i0	518376000.00
molecular_weight	172530.0 kDa
excluded_volume	210130 Å³
envelope_volume	303260 Å³
shell_volume	62378 Å³
envelope_diameter	160.2 Å
shell_rg	44.97 Å
envelope_rg	42.62 Å
shape_rg	41.79 Å
total_rg	42.01 Å
total_atoms	12029
n_residues	1421
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	151.3 Å
rg_real	42.52 Å
rg_real_error	1.55 Å
i0_real	5.1840e+08
i0_real_error	1.0410e+07
rg_reciprocal	42.36 Å
i0_reciprocal	518300000.0000
total_estimate	0.8551
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	45.0 Å
skewness	0.486
kurtosis	-0.116
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	86770000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.886

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	RNA-directed RNA polymerase nsp12
formula_weight	110424.9 kDa
ec_number	2.7.7.48,2.7.7.50
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	12029

MGSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQENLYFQGSWSHPQFEKGGSGSSWSHPQFEK

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Non-structural protein 8
formula_weight	21960.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

GAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Non-structural protein 7
formula_weight	9305.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	Primer RNA
formula_weight	9793.9 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	P

CAUUCUCCUAAGAAGCUAUUAAAAUCACAUU

Entity 5 polymer

description	Template RNA
formula_weight	12088.1 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	T

UUUUCCCAAUGUGAUUUUAAUAGCUUCUUAGGAGAAUG

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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resolution	3.00 Å
resolution_method	—
num_particles	740997

fit	/app/data/saxs_computation/pz/9pz0/9pz0.fit
pddf	/app/data/pr_computation/pz/9pz0/9pz0.pr.out
profile	/app/data/saxs_computation/pz/9pz0/9pz0.dat

SARS-CoV-2 core polymerase complex with two UTP incorporation

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)