SAXSdb — 9vs5

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1. Structure Basics

entry_id	9vs5
deposition_date	2025-07-08
title	Structure of Ebinur lake virus polymerase at the elongation state
keywords	Viral protein, polymerase, elongation complex, L protein, RNA, 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	40.62 Å
rg_electron	40.42 Å
i0	828476000.00
molecular_weight	238220.0 kDa
excluded_volume	298940 Å³
envelope_volume	410070 Å³
shell_volume	81055 Å³
envelope_diameter	137.4 Å
shell_rg	48.49 Å
envelope_rg	39.91 Å
shape_rg	40.43 Å
total_rg	40.83 Å
total_atoms	16710
n_residues	2020
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	129.8 Å
rg_real	40.47 Å
rg_real_error	0.84 Å
i0_real	8.2850e+08
i0_real_error	1.3520e+07
rg_reciprocal	40.62 Å
i0_reciprocal	828600000.0000
total_estimate	0.8845
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.9 Å
skewness	0.220
kurtosis	-0.337
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	147300000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.865

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	RNA-directed RNA polymerase L
formula_weight	259757.0 kDa
ec_number	2.7.7.48
mutation	D79A,D92A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	16710

MEDPMYEQFLQRIQAVRTATVAKDISADILEARHDYFGRELCRALDIEYRNNVLLDEIILDVYPGVNLMEYNVPHVTPANYIWTGDMLLILAYKVSVGHDSTEVTYKKYTTLILPVMQEIGINTEICIIRANPVTNQISIVGEQFKRLFPTIPVELNFARFFELRKMLLDKFADDEEFLMMIAHGDFTLTAPWCQDDTPELIDHPIYQEFLGSMPPRFVSMFEEAMDFSAYNAERWNTLLYKIKNLTLEDYQDYLNIKSHNIFNMTGDFMKPTQDEIDIGWESMSKRISQERELTTDINKQKPSIHFIWAQNKDRKLLNSTAKLVFLSNTLQSITEQSTWTDALKAIGVSMDIGNNIGLYENLCAERKLIARSTGKKVNNKRLEAVKIGKALVLWEQQFILANELFKGQERQKFIKNFFGIGKHKTFKDKTSEDLDREKPKILDFNNTRVLMAARTMVNKNKKFLSQDNTLEFDHPIISTYFDQVREASIDTAQVLKKISKTCFWQAITDISTLMRNILAVSQYNRHNTFRVAMCANDSIYGLVFPSSDIKTKRATIVFCIVCMHNSRDDIMDAGALFTTLETKTKTFVSISKAIRLDKERCQRIVSSPGLFILSTLLLYNNNTEISLYDVMNFTFYTSLSITKSMLSLTEPSRYMIMNSLAISSHVRDYIAEKFSPYTKTLFSVYMVNLIKRGCATANEQSEKIQVRNIYLSDYDITQKGINDIRNLDSIWFPGKVNLKEYINQIYLPFYFNAKGLHEKHHVMIDLAKTVLEIEMNQRLDQLGIWSKNEKKQHVNLPILVHSIAKSLILDTSRHNHLRNRVESRNNFRRSISTISTFTSSKSCIKIGEFQDLKTKEFKATKKMNEKINQKFRLANPLFIDDKDADAEIMHCNYDQLKTKVPNYKDYISVKVFDRLYELYKTKELDDKPFIEQAMKMMKEHKEFNFTFFNKGQKTSKDREIFVGEFEAKMCMYVVERISKERCKLNEDEMISEPGDTKLRILEKKAEEEIRYIVEKTKDSILKGDPAHALKLEINADMSKWSAQDVFFKYFWLVAMDPILYPSEKKRILYFMCNYMQKNLILPDDLLSNIMDQRRPYENDIILESTNGLAQNFVQIKRNWLQGNFNYMSSYVHSCAMLVYKDVAKEAVKLLDGNCLVNSMVHSDDNQTSLSIIQNKLKDNMIIEYVAKLFEAVCLAFGCQANMKKTYITHTCKEFVSLFNLHGEPLSIYGRFLLPSVGDCAYIGPYEDLASRLSAAQQSLKHGCPPSYVWVAISCSHWITHFTYNMMHDQVNSPMQYLPFEDRFQVPTELNGYLSAPLYLIALIGIEADNLWFLLNILKKLVPLDKQKETIQTQFTAIQDNINKLTPSELFRLKLLRYLTLDTEITSDSNMGETSDMRSRSLLTPRKFTTAGSLNKLVSYNDFKNAMNTNEFQENLEYMEMNPELLVTKGENKEQYINSILFRYNSKRFKESLSIQAPSQLFVEQILFSHKPIIDYSSIFDKLASMAETEIIENLPDIIGRVTYPQAYQMITRDITQLPLDIDDIKIVFKYCVLNDPLIITAANTSLLCVRGAPQDRTGLSACQMPEFRNMKLIHHSPALVLKAFSKGTVDIPGADPVELEKDLLHLKEFVENTGIQEKIQMNIDNPPKHLQGTEVLIYKIRELTKLYQVCYDYVKSTEHKVKVFILPMKSYTSIEFCTLIQGNTISDSKWYTMHYLKQVLGGTMKGHMMTTSTSEQVIAAECFRVLTHFADAFVEEGSRVSFLNEILDKFTYKNVSVNYLLNVLLASSNRLDFIPLLFRTKMLTQQDLNKFDALKTNERVSWNNWQTNRGLNSGIIDLTISGYLRSIRIVGEDNKLKIAELTIPNFLPNTIFHAGNKLLNSRHNLKFEYMEEYVLDDKYNYYITYQKKRANLYTYQVSTVDHIWRRNEEGNQKRGKRYNKMVPVCPVVVSSRDEMFKISMQNVFSLNLTNFNLTKLFVSPDEVATIKKAHMSKMMFFSGPQIKAGIIDLTTLMRTQELLTLNYDNLCKSSIIPFCRILACNGEEPGELIFLSDEVMEFTISEEIESMPIFTIRYQKRGNSSMTYKNAIRTLVANGVDEIKEVFDFSGEGFYSKKNLGIINTICSTIEVLETNEWSTILLNSFHIAMLLENMDREFHLFSMPGAFFSNVANGTINWTKLLKFVKSLPAVKKEPWSMMMERFIEKTVYLIEREINKEVDFNDFLEELEYQSGKSMFTFF

Source

organism	Ebinur lake virus
ncbi_taxonomy_id	1501396
host_organism	Pichia

Entity 2 polymer

description	;RNA (5'-R(GPGPAPUPAPAPAPAPAPUPAPAP*U)-3') ;
formula_weight	4197.6 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	P

GGAUAAAAAUAAU

Entity 3 polymer

description	;RNA (5'-R(GPUPAPUPAPUPCPUPCPCPAPUPUPAPUPUPUPUPUPAPUPCP*C)-3') ;
formula_weight	7146.2 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	T

GUAUAUCUCCAUUAUUUUUAUCC

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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	3.310 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.31 Å
resolution_method	—
num_particles	217551

fit	/app/data/saxs_computation/vs/9vs5/9vs5.fit
pddf	/app/data/pr_computation/vs/9vs5/9vs5.pr.out
profile	/app/data/saxs_computation/vs/9vs5/9vs5.dat

Structure of Ebinur lake virus polymerase at the elongation state

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)