SAXSdb — 9vul

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1. Structure Basics

entry_id	9vul
deposition_date	2025-07-13
title	Cryo-EM structure of the human measles virus RNA-dependent RNA polymerase bound to allosteric inhibitor ERDRP-0519
keywords	Measles virus RNA-dependent RNA polymerase complex bound to allosteric inhibitor ERDRP-0519, 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	38.36 Å
rg_electron	37.73 Å
i0	883004000.00
molecular_weight	161200.0 kDa
excluded_volume	155920 Å³
envelope_volume	299030 Å³
shell_volume	64925 Å³
envelope_diameter	137.5 Å
shell_rg	44.81 Å
envelope_rg	37.23 Å
shape_rg	37.72 Å
total_rg	38.07 Å
total_atoms	12206
n_residues	1528
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	126.7 Å
rg_real	38.24 Å
rg_real_error	1.00 Å
i0_real	8.8300e+08
i0_real_error	1.4670e+07
rg_reciprocal	38.31 Å
i0_reciprocal	883100000.0000
total_estimate	0.8643
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.5 Å
skewness	0.310
kurtosis	-0.089
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	89440000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.836

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Maltose/maltodextrin-binding periplasmic protein,Phosphoprotein
formula_weight	66334.4 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	12206

MGSSHHHHHHGTKTEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTGTDYDIPTTLEVLFQGPLGSGDYYDDELFSDVQDIKTALAKIHEDNQKIISKLESLLLLKGEVESIKKQINRQNISISTLEGHLSSIMIAIPGLGKDPNDPTADVEINPDLKPIIGRDSGRALAEVLKKPVASRQLQGMTNGRTSSRGQLLKEFQPKPIGKKMSSAVGFVPDTGPASRSVIRSIIKSSRLEEDRKRYLMTLLDDIKGANDLAKFHQMLMKIIMK

Source

organism	Measles virus genotype A-vaccine
ncbi_taxonomy_id	1056493
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA polymerase L,Strep II and FLAG tag
formula_weight	297006.9 kDa
ec_number	2.7.7.48,3.6.1.-,2.7.7.88,2.1.1.375
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MGSSHHHHHHGTKTEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTGTDYDIPTTLEVLFQGPLGSMDSLSVNQILYPEVHLDSPIVTNKIVAILEYARVPHAYSLEDPTLCQNIKHRLKNGFSNQMIINNVEVGNVIKSKLRSYPAHSHIPYPNCNQDLFNIEDKESTRKIRELLKKGNSLYSKVSDKVFQCLRDTNSRLGLGSELREDIKEKVINLGVYMHSSQWFEPFLFWFTVKTEMRSVIKSQTHTCHRRRHTPVFFTGSSVELLISRDLVAIISKESQHVYYLTFELVLMYCDVIEGRLMTETAMTIDARYTELLGRVRYMWKLIDGFFPALGNPTYQIVAMLEPLSLAYLQLRDITVELRGAFLNHCFTEIHDVLDQNGFSDEGTYHELIEALDYIFITDDIHLTGEIFSFFRSFGHPRLEAVTAAENVRKYMNQPKVIVYETLMKGHAIFCGIIINGYRDRHGGSWPPLTLPLHAADTIRNAQASGEGLTHEQCVDNWKSFAGVKFGCFMPLSLDSDLTMYLKDKALAALQREWDSVYPKEFLRYDPPKGTGSRRLVDVFLNDSSFDPYDVIMYVVSGAYLHDPEFNLSYSLKEKEIKETGRLFAKMTYKMRACQVIAENLISNGIGKYFKDNGMAKDEHDLTKALHTLAVSGVPKDLKESHRGGPVLKTYSRSPVHTSTRNVRAAKGFIGFPQVIRQDQDTDHPENMEAYETVSAFITTDLKKYCLNWRYETISLFAQRLNEIYGLPSFFQWLHKRLETSVLYVSDPHCPPDLDAHIPLYKVPNDQIFIKYPMGGIEGYCQKLWTISTIPYLYLAAYESGVRIASLVQGDNQTIAVTKRVPSTWPYNLKKREAARVTRDYFVILRQRLHDIGHHLKANETIVSSHFFVYSKGIYYDGLLVSQSLKSIARCVFWSETIVDETRAACSNIATTMAKSIERGYDRYLAYSLNVLKVIQQILISLGFTINSTMTRDVVIPLLTNNDLLIRMALLPAPIGGMNYLNMSRLFVRNIGDPVTSSIADLKRMILASLMPEETLHQVMTQQPGDSSFLDWASDPYSANLVCVQSITRLLKNITARFVLIHSPNPMLKGLFHDDSKEEDEGLAAFLMDRHIIVPRAAHEILDHSVTGARESIAGMLDTTKGLIRASMRKGGLTSRVITRLSNYDYEQFRAGMVLLTGRKRNVLIDKESCSVQLARALRSHMWARLARGRPIYGLEVPDVLESMRGHLIRRHETCVICECGSVNYGWFFVPSGCQLDDIDKETSSLRVPYIGSTTDERTDMKLAFVRAPSRSLRSAVRIATVYSWAYGDDDSSWNEAWLLARQRANVSLEELRVITPISTSTNLAHRLRDRSTQVKYSGTSLVRVARYTTISNDNLSFVISDKKVDTNFIYQQGMLLGLGVLETLFRLEKDTGSSNTVLHLHVETDCCVIPMIDHPRIPSSRKLELRAELCTNPLIYDNAPLIDRDTTRLYTQSHRRHLVEFVTWSTPQLYHILAKSTALSMIDLVTKFEKDHMNEISALIGDDDINSFITEFLVIEPRLFTIYLGQCAAINWAFDVHYHRPSGKYQMGELLSSFLSRMSKGVFKVLVNALSHPKIYKKFWHCGIIEPIHGPSLDAQNLHTTVCNMVYTCYMTYLDLLLNEELEEFTFLLCESDEDVVPDRFDNIQAKHLCVLADLYCQPGACPPIRGLRPVEKCAVLTDHIKAEARLSPAGSSWNINPIIVDHYSCSLTYLRRGSIKQIRLRVDPGFIFDALAEVNVSQPKIGSNNISNMSIKAFRPPHDDVAKLLKDINTSKHNLPISGGNLANYEIHAFRRIGLNSSACYKAVEISTLIRRCLEPGEDGLFLGEGSGSMLITYKEILKLNKCFYNSGVSANSRSGQRELAPYPSEVGLVEHRMGVGNIVKVLFNGRPEVTWVGSVDCFNFIVSNIPTSSVGFIHSDIETLPNKDTIEKLEELAAILSMALLLGKIGSILVIKLMPFSGDFVQGFISYVGSYYREVNLVYPRYSNFISTESYLVMTDLKANRLMNPEKIKQQIIESSVRTSPGLIGHILSIKQLSCIQAIVGDVVSRGDINPTLKKLTPIEQVLINCGLAINGPKLCKELIHHDVASGQDGLLNSILILYRELARFKDNRRSQQGMFHAYPVLVSSRQRELISRITRKFWGHILLYSGNRKLINKFIQNLKSGYLILDLHQNIFVKNLSKSEKQIIMTGGLKREWVFKVTVKETKEWYKLVGYSALIKDSRENLYFQGSGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGSDYKDDDDK

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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	3.130 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.13 Å
resolution_method	—
num_particles	177478

fit	/app/data/saxs_computation/vu/9vul/9vul.fit
pddf	/app/data/pr_computation/vu/9vul/9vul.pr.out
profile	/app/data/saxs_computation/vu/9vul/9vul.dat

Cryo-EM structure of the human measles virus RNA-dependent RNA polymerase bound to allosteric inhibitor 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)