SAXSdb — 9x5r

▼

1. Structure Basics

entry_id	9x5r
deposition_date	2025-10-13
title	Cryo-EM structure of Borna disease virus RNA-directed RNA polymerase in complex with Suramin
keywords	Polymerase, Complex, Inhibitor, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.59 Å
rg_electron	31.64 Å
i0	301468000.00
molecular_weight	141550.0 kDa
excluded_volume	178190 Å³
envelope_volume	222760 Å³
shell_volume	55866 Å³
envelope_diameter	103.0 Å
shell_rg	40.71 Å
envelope_rg	31.19 Å
shape_rg	31.63 Å
total_rg	32.43 Å
total_atoms	9940
n_residues	1231
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

▼

3. P(r) Analysis (GNOM)

dmax	96.0 Å
rg_real	32.29 Å
rg_real_error	0.47 Å
i0_real	3.0150e+08
i0_real_error	3.9990e+06
rg_reciprocal	32.42 Å
i0_reciprocal	301500000.0000
total_estimate	0.9062
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	43.1 Å
skewness	0.048
kurtosis	-0.561
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	88240000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.958

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	RNA-directed RNA polymerase L
formula_weight	194970.9 kDa
ec_number	2.7.7.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9940

MSFHASLLREEETPRPVAGINRTDQSLKNPLLGTEVSFCLKSSSLPHHVRALGQIKARNLASCDYYLLFRQVVLPPEVYPIGVLIRAAEAILTVIVSAWKLDHMTKTLYSSVRYALTNPRVRAQLELHIAYQRIVGQVSYSREADIGPKRLGNMSLQFIQSLVIATIDTTSCLMTYNHFLAAADTAKSRCHLLIASVVQGALWEQGSFLDHIINMIDIIDSINLPHDDYFTIIKSIFPYSQGLVMGRHNVSVSSDFASVFAIPELCPQLDSLLKKLLQLDPVLLLMVSSVQKSWYFPEIRMVDGSREQLHKMRVELETPQALLSYGHTLLSIFRAEFIKGYVSKNAKWPPVHLLPGCDKSIKNARELGRWSPAFDRRWQLFEKVVILRIADLDMDPDFNDIVSDKAIISSRRDWVFEYNAAAFWKKYGERLERPPARSGPSRLVNALIDGRLDNIPALLEPFYRGAVEFEDRLTVLVPKEKELKVKGRFFSKQTLAIRIYQVVAEAALKNEVMPYLKTHSMTMSSTALTHLLNRLSHTITKGDSFVINLDYSSWCNGFRPELQAPICRQLDQMFNCGYFFRTGCTLPCFTTFIIQDRFNPPYSLSGEPVEDGVTCAVGTKTMGEGMRQKLWTILTSCWEIIALREINVTFNILGQGDNQTIIIHKSASQNNQLLAERALGALYKHARLAGHNLKVEECWVSDCLYEYGKKLFFRGVPVPGCLKQLSRVTDSTGELFPNLYSKLACLTSSCLSAAMADTSPWVALATGVCLYLIELYVELPPAIIQDESLLTTLCLVGPSIGGLPTPATLPSVFFRGMSDPLPFQLALLQTLIKTTGVTCSLVNRVVKLRIAPYPDWLSLVTDPTSLNIAQVYRPERQIRRWIEEAIATSSHSSRIATFFQQPLTEMAQLLARDLSTMMPLRPRDMSALFALSNVAYGLSIIDLFQKSSTVVSASQAVHIEDVALESVRYKESIIQGLLDTTEGYNMQPYLEGCTYLAAKQLRRLTWGRDLVGVTMPFVAEQFHPHSSVGAKAELYLDAIIYCPQETLRSHHLTTRGDQPLYLGSNTAVKVQRGEITGLAKSRAANLVKDTLVLHQWYKVRKVTDPHLNTLMARFLLEKGYTSDARPSIQGGTLTHRLPSRGDSRQGLTGYVNILSTWLRFSSDYLHSFSKSSDDYTIHFQHVFTYGCLYADSVIRSGGVISTPYLLSASCKTCFEKIDSEEFVLACEPQYRGAEWLISKPVTVPEQITDAEVEFDPCVSASYCLGILIGKSFLVDIRASGHDIMEQRTWANLERFSVSDMQKLPWSIVIRSLWRFLIGARLLQFEKAGLIRMLYAATGPTFSFLMKVFQDSALLMDCAPLDRLSPRINFHSRGDLVAKLVLLPFINPGIVEIEVSGINSKYHAVSEANMDLYIAAAKSVGVKPTQFVEETNDFTARGHHHGCYSLSWSKSRNQSQVLKMVVRKLKLCVLYIYPTVDPAVALDLCHLPALTIILVLGGDPAYYERLLEMDLCGAVSSRVDIPHSLAARTHRGFAVGPDAGPGVIRLDRLESVCYAHPCLEELEFNAYLDSELVDISDMCCLPLATPCKALFRPIYRSLQSFRLALMDNYSFVMDLIMIRGLDIRPHLEEFDELLVVGQHILGQPVLVEVVYYVGVVRKRPVLARHPWSADLKRITVGGRAPCPSAARLRDEDCQGSLLVGLPAGLTQLLIIDWSHPQFEKGSSGGSSGSSGGAWSHPQFEK

Source

organism	Borna disease virus-V
ncbi_taxonomy_id	928296
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Phosphoprotein
formula_weight	22515.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MATRPSSLVDSLEDEEDPQTLRRERPGSPRPRKVPRNALTQPVDQLLKDLRKNPSMISDPDQRTGREQLSNDELIKKLVTELAENSMIEAEEVRGTLGDISARIEAGFESLSALQVETIQTAQRCDHSDSIRILGENIKILDRSMKTMMETMKLMMEKVDLLYASTAVGTSAPMLPSHPAPPRIYPQLPSAPTTDEWDIIP

Source

organism	Borna disease virus-V
ncbi_taxonomy_id	928296
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	;8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID ;
formula_weight	1297.3 kDa
src_method	syn
entity_count	3

▶

6. Citations (1)

▶

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	2.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.70 Å
resolution_method	—
num_particles	214426

fit	/app/data/saxs_computation/x5/9x5r/9x5r.fit
pddf	/app/data/pr_computation/x5/9x5r/9x5r.pr.out
profile	/app/data/saxs_computation/x5/9x5r/9x5r.dat

Cryo-EM structure of Borna disease virus RNA-directed RNA polymerase in complex with Suramin

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)