SAXSdb — 9vfr

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1. Structure Basics

entry_id	9vfr
deposition_date	2025-06-11
title	Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1
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	33.70 Å
rg_electron	33.17 Å
i0	223557000.00
molecular_weight	120110.0 kDa
excluded_volume	150030 Å³
envelope_volume	187850 Å³
shell_volume	46785 Å³
envelope_diameter	121.0 Å
shell_rg	40.14 Å
envelope_rg	33.60 Å
shape_rg	33.17 Å
total_rg	33.70 Å
total_atoms	8479
n_residues	1119
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	114.2 Å
rg_real	33.70 Å
rg_real_error	0.92 Å
i0_real	2.2360e+08
i0_real_error	3.7760e+06
rg_reciprocal	33.70 Å
i0_reciprocal	223600000.0000
total_estimate	0.8794
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.9 Å
skewness	0.360
kurtosis	-0.278
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	28770000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.937

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	8479

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	Kremen protein 1
formula_weight	32728.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

PECFTANGADYRGTQNWTALQGGKPCLFWNETFQHPYNTLKYPNGEGGLGEHNYCRNPDGDVSPWCYVAEHEDGVYWKYCEIPACQMPGNLGCYKDHGNPPPLTGTSKTSNKLTIQTCISFCRSQRFKFAGMESGYACFCGNNPDYWKYGEAASTECNSVCFGDHTQPCGGDGRIILFDTLVGACGGNYSAMSSVVYSPDFPDTYATGRVCYWTIRVPGASHIHFSFPLFDIRDSADMVELLDGYTHRVLARFHGRSRPPLSFNVSLDFVILYFFSDRINQAQGFAVLYQAVK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 6 non-polymer

description	STEARIC ACID
formula_weight	284.5 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	MYRISTIC ACID
formula_weight	228.4 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	2

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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	2.55 Å
resolution_method	—
num_particles	19306

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

Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1

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

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)