SAXSdb — 9vy0

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1. Structure Basics

entry_id	9vy0
deposition_date	2025-07-20
title	Cryo-EM Structure of Peste Des Petits Ruminants Virus Polymerase in complex with ERDRP-0519
keywords	Polymerase, inhibitor, complex, RNA, 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	41.76 Å
rg_electron	41.96 Å
i0	876871000.00
molecular_weight	161710.0 kDa
excluded_volume	156720 Å³
envelope_volume	289820 Å³
shell_volume	61493 Å³
envelope_diameter	167.0 Å
shell_rg	44.21 Å
envelope_rg	42.49 Å
shape_rg	41.97 Å
total_rg	42.04 Å
total_atoms	12253
n_residues	1540
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	155.6 Å
rg_real	42.31 Å
rg_real_error	1.50 Å
i0_real	8.7690e+08
i0_real_error	1.5500e+07
rg_reciprocal	41.76 Å
i0_reciprocal	876400000.0000
total_estimate	0.7584
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.1 Å
skewness	0.896
kurtosis	0.794
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	61840000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.424; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.646

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	RNA-directed RNA polymerase L
formula_weight	247576.3 kDa
ec_number	2.7.7.48,3.6.1.-,2.7.7.88,2.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	12256

MDSLSVNQVLYPEVHLDSPIVTNKLVAILEYSGIDHNYVLEDQTLVKNIRYRLGCGFSNQMIINNRGVGETVNSKLKSYPHNRHIIYPDCNKELFCIKDSCISKKLSELFKKGNSLYSKISHQVLDCLKRVNGKLGLGTDLTYGLKEGILDLGLHMHSSQWFETFLFWFTIKTEMRSMIKEQSHICHKRRYNPIFVSGDAFEVLVSRDLVVIIDKNTQYVFYLTFELVLMYCDVIEGRLMTETAMAIDQRYSELLSRVRYLWDLIDGFFPTLGNTTYQVVALLEPLSLAYLQLQDVTLELRGAFLDHCFKELYEILEHCGIDTEGTYNSITEGLDYVFITHDIHLTGEIFSFFRSFGHPRLEAVTAAENVRKHMNQPKVISYETMMKGHAVFCGIIINGFRDRHGGSWPPVALPEHASAAIRNAQASGEGLTHDLCIDNWKSFVGFKFGCFMPLSLDSDLTMYLKDKALAALKNEWDSVYPKEYLRYNPPRGTESRRLVEVFLNDSSFDPYNMIMYVVNGSYLKDPEFNLSYSLKEKEIKETGRLFAKMTYKMRACQVIAENLISNGVGKYFRDNGMAKDEHDLTKALHTLAVSGVPKNNKDNHRGGPPRRTTNREVRSSQDTKTQNRDKVQGGPVYNYLRCQPISPDQGESYETVSAFITADLKKYCLNWRYETISIFAQRLNEIYGLPSFFQWLHRILEKSVLYVSDPHCPPDLDNHIPLDSVPNAQIFIKYPMGGIEGYCQKLWTISTIPYLYLAAYESGVRIASLVQGDNQTIAVTKRVPSSWPYSLKKREASKAAQNYFVVLRQRLHDVGHHLKANETIVSSHFFVYSKGIYYDGLLVSQSLKSIARCVFWSETIVDETRAACSNIATTVAKSIERGYDRYLAYSLNILKIFQQILISLNFTINTTMTQDVVAPIIENGDLLIRMALLPAPIGGLNYLNMSRLFVRNIGDPVTSSIADLKRMIDAGLMPEETLHQVMTQTPGESSYLDWASDPYSANLPCVQSITRLLKNITARYILISSPNPMLKGLFHEGSRDEDEELASFLMDRHIIVPRAAHEILDHSITGAREAIAGMLDTTKGLIRTSMKRGGLTPRVLARLSNYDYEQFRSGITLLTKKGQCYLIDKDSCSVQLAIALRSHMWARLARGRPIYGLEVPDILESMNGYLIKRHESCAICETGSSHYGWFFVPAGCQLDDVSRETSALRVPYVGSTTEERTDMKLAFVRSPSRSLKSAVRIATVYSWAYGDDEKSWGEAWMLARQRANITLDELRMITPVSTSTNLAHRLRDRSTQVKYSGTSLVRVARYTTISNDNLSFVISEKKVDTNFIYQQGMLLGLGILENLFRLEATTGVSNTVLHLHVETECCVVPMVDHPRIPSLRNIKVTDELCTNPLIYDRSPIIEHDATRLYSQSHRRHLVEFVTWSTSQLYHILAKSTAMSMIELITRFEKDHMNEIAALIGDDDINSFITEFLLVEPRLFIVYLGQCAAINWAFDIHYHRPSGKHQMGELLYSLLSRMSKGVYKIFTNALSHPKVYKKFWRSGVIEPIHGPSLDTQNLHVTVCDMIYGSYVTYLDLLLNDELDDYPYLLCESDEDVVTDRFDNIQAKHLCVLADVYCSSKRCPSIIGMSPIEKCTILTHYIKGESVQSPSGTSWNTDPLVVDHYSCSLTYLRCGSIKQIRLRVDPGFVFEALTDVDFKQPRKAKLDISVVGLTDFSPPCDNVGDFLGTINTLRHNLPVTGTGVSNYEVHAYRRIGLNSSACYKAVEISTLIRPSLEVGEHGLFLGEGSGSMLAAYKEVLKLANCYYNSGVTAEGRAGQREISPYPSEMSLVENQMGIERSVKVLFNGKPEVTWVGTTDCYKYIISNIQTSSLGFIHSDIETLPTKDAVEKLEEFASILSLSLILGKIGSITVVKVMPISGDFTQGFIAYAIQYFRESLLAYPRYSNFISTECYLIMIGLKANRLINPEAIKQSIIRAGVRTAPGLVSHILSGKQKGCIQSFLGDPYIQGDFNKHLKSLTPIEKILVNCGLSINGTKICRDLIHHDIASGPDGLMSSTIILYRELAHFKDNIRSQHGMFHPYPVLANSRQRELILRIAKKFWGYVLLYSDDPALIRQTIKNLKRNHLTFDLHSNPFIKGLSKAEKLLVRTSSLRREWLFTLDTKEVKEWFKLVGYSALIRG

Source

organism	peste-des-petits-ruminants virus
ncbi_taxonomy_id	2593991
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Phosphoprotein
formula_weight	54857.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,C,D,E

MAEEQAYHVNKGLECIKSLKASPPDLSTIRDTIESWREGLSPSGRATPNPDTSEGDHQSINQSCSPAIGPNKVYLSPGDNLGFREITGNDCEAGLGGVQGKRSNSQVQRYYVYSHGGEEIEGLEDADSLVVQADPPVANVFNGGEDGSDDSDVDSGPDDPSRDTLYDRGSVAGNDVARSTDVEKLEGADIQEVLNSQKGKGGRFQGGKTLRVPEIPDVKHSRPSAQSIKKGTDGNSVSSGTVTECLSISGATQAVPESRWESSEQNASVGSVLKSARSAETIQGLTQESGTIASLTQPKENDSEYEYEDDLFKEIQDIRASIAKIHDDNKTILSKLDSILLLKGEVDTIKKQISKQNISISTIEGHLSSIMIAIPGFGKDIKDPTSEVELNPDLRPIISRDSGRALAEVLKKPAVDRSQKIGTKANSSSKGQLLKDLQLKPVDKQASSAIGFVPSDHESSRNVIRSIIKSSKLNTDHKDYLLDLLNDVKGSKDLKEFHKMLTAILAKHP

Source

organism	peste-des-petits-ruminants virus
ncbi_taxonomy_id	2593991
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	2-methyl-~{N}-[4-[(2~{S})-2-(2-morpholin-4-ylethyl)piperidin-1-yl]sulfonylphenyl]-5-(trifluoromethyl)pyrazole-3-carboxamide
formula_weight	529.6 kDa
src_method	syn
entity_count	1

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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	2.710 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.71 Å
resolution_method	—
num_particles	3880076

fit	/app/data/saxs_computation/vy/9vy0/9vy0.fit
pddf	/app/data/pr_computation/vy/9vy0/9vy0.pr.out
profile	/app/data/saxs_computation/vy/9vy0/9vy0.dat

Cryo-EM Structure of Peste Des Petits Ruminants Virus Polymerase in complex with ERDRP-0519

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

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)