SAXSdb — 9vfu

▼

1. Structure Basics

entry_id	9vfu
deposition_date	2025-06-11
title	Structure of mature CVA6 virus complexed with 1F4 Fab
keywords	coxsackievirus A6, KRM1, receptor, VIRUS; VIRUS
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	31.22 Å
rg_electron	30.44 Å
i0	184722000.00
molecular_weight	109350.0 kDa
excluded_volume	136930 Å³
envelope_volume	168000 Å³
shell_volume	44530 Å³
envelope_diameter	108.1 Å
shell_rg	38.55 Å
envelope_rg	31.13 Å
shape_rg	30.42 Å
total_rg	31.14 Å
total_atoms	7728
n_residues	1036
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	97.6 Å
rg_real	31.11 Å
rg_real_error	0.55 Å
i0_real	1.8470e+08
i0_real_error	2.7630e+06
rg_reciprocal	31.16 Å
i0_reciprocal	184700000.0000
total_estimate	0.9044
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	36.4 Å
skewness	0.235
kurtosis	-0.465
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	34500000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.943

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	Genome polyprotein
formula_weight	33568.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7728

NDPITNAVESAVSALADTTISRVTAANTAASTHSLGTGRVPALQAAETGASSNSSDENLIETRCVMNRNGVNEASVEHFYSRAGLVGVVEVKDSGTSLDGYTVWPIDVMGFVQQRRKLELSTYMRFDAEFTFVSNLNNSTTPGMLLQYMYVPPGAPKPDSRKSYQWQTATNPSVFAKLSDPPPQVSVPFMSPATAYQWFYDGYPTFGEHKQATNLQYGQCPNNMMGHFAIRTVSESTTGKNIHVRVYMRIKHVRAWVPRPLRSQAYMVKNYPTYSQTITNTATDRASITTTDYEGGVPASPQRTS

Entity 2 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

Entity 3 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 4 polymer

description	Genome polyprotein
formula_weight	7503.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MGAQVSTQKSGSHETRNVATEGSTINFTNINYYKDSYAASASRQDFAQDPAKFTRPVLDAIREAAAPLQ

Entity 5 polymer

description	VH
formula_weight	12667.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

QVQLQQSGAELVKPGASVKLSCKASGYTFTSYYMYWVKQRPGQGLEWIGEINPSNGGTNFNEKFKSKATLTVDKSSSTAYMQLSSLTSEDSAVYYCTRYGNYAYWGQGTLVTVSA

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 6 polymer

description	VL
formula_weight	11676.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

DIQMTQSPASLSVSVGETVTITCRASENIYSNLAWYQQKQGKSPQLLVYAATNLADGVPSRFSGSGSGTQYSLKINSLQSEDFGSYYCQHFWGTPWTFGGGTKLEIK

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 7 non-polymer

description	STEARIC ACID
formula_weight	284.5 kDa
src_method	syn
entity_count	1

▶

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	2.110 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.11 Å
resolution_method	—
num_particles	81877

fit	/app/data/saxs_computation/vf/9vfu/9vfu.fit
pddf	/app/data/pr_computation/vf/9vfu/9vfu.pr.out
profile	/app/data/saxs_computation/vf/9vfu/9vfu.dat

Structure of mature CVA6 virus complexed with 1F4 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)