SAXSdb — 9rim

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1. Structure Basics

entry_id	9rim
deposition_date	2025-06-11
title	EV-A71 (genotype B5) in complex with 16-3-4D Fab
keywords	Hand-foot-and-mouth disease, HFMD, enterovirus 71 (EV-A71), Human antibody, VIRUS, 16-3-4D; VIRUS
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	33.34 Å
rg_electron	32.77 Å
i0	213787000.00
molecular_weight	117730.0 kDa
excluded_volume	147260 Å³
envelope_volume	185610 Å³
shell_volume	46958 Å³
envelope_diameter	128.2 Å
shell_rg	39.75 Å
envelope_rg	33.32 Å
shape_rg	32.75 Å
total_rg	33.36 Å
total_atoms	8297
n_residues	1073
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	116.7 Å
rg_real	33.32 Å
rg_real_error	0.92 Å
i0_real	2.1380e+08
i0_real_error	3.5710e+06
rg_reciprocal	33.33 Å
i0_reciprocal	213800000.0000
total_estimate	0.6845
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	39.7 Å
skewness	0.345
kurtosis	-0.315
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	35350000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 0.214; Positv: 1.000; Valcen: 0.959; Smooth: 0.950

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	VP1
formula_weight	32748.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8297

GDRVADVIESSIGDSVSRALTQALPAPTGQNTQVSSHRLDTGEVPALQAAEIGASSNTSDESMIETRCVLNSHSTAETTLDSFFSRAGLVGEIDLPLEGTTNPNGYANWDIDITGYAQMRRKVELFTYMRFDAEFTFVACTPTGQVVPQLLQYMFVPPGAPKPDSRESLAWQTATNPSVFVKLTDPPAQVSVPFMSPASAYQWFYDGYPTFGEHKQEKDLEYGACPNNMMGTFSVRTVGSSKSKYPLVVRIYMRMKHVRAWIPRPMRNQNYLFKANPNYAGNSIKPTGTSRTAITTL

Entity 2 polymer

description	Genome polyprotein
formula_weight	27814.3 kDa
ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SPSAEACGYSDRVAQLTIGNSTITTQEAANIIVGYGEWPSYCSDDDATAVDKPTRPDVSVNRFYTLDTKLWEKSSKGWYWKFPDVLTETGVFGQNAQFHYLYRSGFCIHVQCNASKFHQGALLVAILPEYVIGTVAGGTGTEDSHPPYKQTQPGADGFELQHPYVLDAGIPISQLTICPHQWINLRTNNCATIIVPYMNTLPFDSALNHCNFGLLVVPISPLDFDQGATPVIPITITLAPMCSEFAGLRQAVTQ

Entity 3 polymer

description	Genome polyprotein
formula_weight	26558.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GFPTEPKPGTNQFLTTDDGVSAPILPNFHPTPCIHIPGEVRNLLELCQVETILEVNNVPTNATSLMERLRFPVSAQAGKGELCAVFRADPGRDGPWQSTMLGQLCGYYTQWSGSLEVTFMFTGSFMATGKMLIAYTPPGGPLPKDRATAMLGTHVIWDFGLQSSVTLVIPWISNTHYRAHARDGVFDYYTTGLVSFWYQTNYVVPIGAPNTAYIIALAAAQKNFTMKLCKDTSHILQTASIQ

Entity 4 polymer

description	Capsid protein
formula_weight	7501.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MGSQVSTQRSGSHENSNSATEGSTINYTTINYYKDSYAATAGKQSLKQDPDKFANPVKDIFTEMAAPLK

Entity 5 polymer

description	light chain
formula_weight	23097.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

QSVLTQPPSASETPGQRVTISCSGSRSNIGRKTVNWYQRLPGTAPKLLIYSDTQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNNWVFGGGTKLTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 6 polymer

description	heavy chain
formula_weight	25252.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QLQLQESGPGLVKPSETLSLTCSVSGGSISISSYYWGWIRLPPGKGLEWIGSVYYSGPTYHNPSLKSRVTISLDTANNQFSLKLTSVTGADAAVYYCARHVPVAGFGYYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKHHHHHH

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 7 non-polymer

description	SPHINGOSINE
formula_weight	299.5 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	3.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.00 Å
resolution_method	—
num_particles	26427

fit	/app/data/saxs_computation/ri/9rim/9rim.fit
pddf	/app/data/pr_computation/ri/9rim/9rim.pr.out
profile	/app/data/saxs_computation/ri/9rim/9rim.dat

EV-A71 (genotype B5) in complex with 16-3-4D Fab

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 (7)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)