SAXSdb — 9vg1

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1. Structure Basics

entry_id	9vg1
deposition_date	2025-06-12
title	Structure of CVA6 empty capsid complexed with 3H7 Fab
keywords	coxsackievirus A6, KRM1, receptor, VIRUS; 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	32.10 Å
rg_electron	31.50 Å
i0	129786000.00
molecular_weight	91014.0 kDa
excluded_volume	113850 Å³
envelope_volume	148130 Å³
shell_volume	39568 Å³
envelope_diameter	115.9 Å
shell_rg	37.92 Å
envelope_rg	32.10 Å
shape_rg	31.48 Å
total_rg	32.11 Å
total_atoms	6432
n_residues	866
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	105.3 Å
rg_real	32.14 Å
rg_real_error	1.00 Å
i0_real	1.2980e+08
i0_real_error	2.1360e+06
rg_reciprocal	32.13 Å
i0_reciprocal	129800000.0000
total_estimate	0.8160
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.367
kurtosis	-0.411
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	21990000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	VL
formula_weight	11801.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D
atom_count	6443

DIQMTQSPSSLSASLGERVSLTCRASQDIGSRLNWLQQEPDGTIKRLIYATSSLDSGVPKRFSGSRSGSYYSLTISSLESEDFVDYYCLQYAGFPWTFGGGTKLEIK

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 2 polymer

description	VH
formula_weight	13671.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

EVKLVESGGGLVKPGGSLKLSCAASGFAFSTYDMSWVRQTPEKRLEWVATISSGGSYTYYPDSVKGRFTISRDNARNTLYLQMSSLRSEDTALYYCARGGPYDYDGSFYTMDYWGQGTSVTVSS

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 3 polymer

description	Genome polyprotein
formula_weight	33568.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

NDPITNAVESAVSALADTTISRVTAANTAASTHSLGTGRVPALQAAETGASSNSSDENLIETRCVMNRNGVNEASVEHFYSRAGLVGVVEVKDSGTSLDGYTVWPIDVMGFVQQRRKLELSTYMRFDAEFTFVSNLNNSTTPGMLLQYMYVPPGAPKPDSRKSYQWQTATNPSVFAKLSDPPPQVSVPFMSPATAYQWFYDGYPTFGEHKQATNLQYGQCPNNMMGHFAIRTVSESTTGKNIHVRVYMRIKHVRAWVPRPLRSQAYMVKNYPTYSQTITNTATDRASITTTDYEGGVPASPQRTS

Entity 4 polymer

description	Genome polyprotein
formula_weight	26324.8 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	C

GFPTELKPGTNQFLTTDDGTSPPILPGFEPTPLIHIPGEFTSLLDLCQVETILEVNNTTGTTGVSRLLIPVRAQNNVDQLCASFQVDPGRNGPWQSTMVGQICRYYTQWSGSLKVTFMFTGSFMATGKMLIAYTPPGSAQPTTREAAMLGTHIVWDFGLQSSVTLVIPWISNTHFRAVKTGGVYDYYATGIVTIWYQTNFVVPPDTPTEANIIALGAAQKNFTLKLCKDTDEIQQTAEYQ

Entity 5 polymer

description	Genome polyprotein
formula_weight	28138.6 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

SPSVEACGYSDRVAQLTVGNSTITTQEAANIVLSYGEWPEYCPSTDATAVDKPTRPDVSVNRFYTLSTKSWKTESTGWYWKFPDVLNDTGVFGQNAQFHYLYRSGFCMHVQCNASKFHQGALLVAAIPEFVIAASSPATKPNSQGLYPDFAHTNPGKDGQEFRDPYVLDAGIPLSQALIFPHQWINLRTNNCATIIMPYINALPFDSALNHSNFGLVVIPISPLKYCNGATTEVPITLTIAPLNSEFSGLRQAIKQ

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6. Citations (1)

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resolution	3.260 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.26 Å
resolution_method	—
num_particles	810

fit	/app/data/saxs_computation/vg/9vg1/9vg1.fit
pddf	/app/data/pr_computation/vg/9vg1/9vg1.pr.out
profile	/app/data/saxs_computation/vg/9vg1/9vg1.dat

Structure of CVA6 empty capsid complexed with 3H7 Fab

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)