SAXSdb — 9vy1

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1. Structure Basics

entry_id	9vy1
deposition_date	2025-07-20
title	Cryo-EM structure of Peste Des Petits Ruminants Virus L Protein bound by Phosphoprotein Tetramer
keywords	Polymerase, inhibitor, Peste Des Petits Ruminants Virus, complex, 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	41.70 Å
rg_electron	42.12 Å
i0	410420000.00
molecular_weight	169640.0 kDa
excluded_volume	214570 Å³
envelope_volume	284480 Å³
shell_volume	60223 Å³
envelope_diameter	165.9 Å
shell_rg	44.15 Å
envelope_rg	42.79 Å
shape_rg	42.06 Å
total_rg	42.48 Å
total_atoms	11937
n_residues	1504
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	156.7 Å
rg_real	42.23 Å
rg_real_error	1.95 Å
i0_real	4.1040e+08
i0_real_error	8.1380e+06
rg_reciprocal	41.71 Å
i0_reciprocal	410200000.0000
total_estimate	0.7580
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.5 Å
skewness	0.889
kurtosis	0.824
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	59960000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.412; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.675

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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	11940

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

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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	2.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.40 Å
resolution_method	—
num_particles	5435091

fit	/app/data/saxs_computation/vy/9vy1/9vy1.fit
pddf	/app/data/pr_computation/vy/9vy1/9vy1.pr.out
profile	/app/data/saxs_computation/vy/9vy1/9vy1.dat

Cryo-EM structure of Peste Des Petits Ruminants Virus L Protein bound by Phosphoprotein Tetramer

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)