SAXSdb — 9vg7

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1. Structure Basics

entry_id	9vg7
deposition_date	2025-06-13
title	Cryo-EM Structure of Rc-o319 Ectodomain trimer
keywords	COMPLEX, VIRAL PROTEIN; VIRAL PROTEIN
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	48.40 Å
rg_electron	47.93 Å
i0	1899810000.00
molecular_weight	364340.0 kDa
excluded_volume	455780 Å³
envelope_volume	609030 Å³
shell_volume	102740 Å³
envelope_diameter	156.6 Å
shell_rg	54.29 Å
envelope_rg	47.33 Å
shape_rg	47.99 Å
total_rg	47.95 Å
total_atoms	25665
n_residues	3225
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	154.7 Å
rg_real	48.27 Å
rg_real_error	1.17 Å
i0_real	1.9000e+09
i0_real_error	3.3010e+07
rg_reciprocal	48.40 Å
i0_reciprocal	1900000000.0000
total_estimate	0.8675
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	56.3 Å
skewness	0.295
kurtosis	-0.403
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	289600000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.595

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Spike glycoprotein
formula_weight	129563.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	25665

CVNITYGSHHLYVSSRTRGVYYPDDAFRSSTNVLHEGFFLPFDSNVTWYSFWNQKYSVATSPFGDGVYFSTIDKSNVVRGWVFGTTLDNDTQSVLLYNDGTHVRVEVCTFHFCPTPVFSASSPHLYSSAFNCTLNYTLASVRADFTEVDGSFKTIREFVFKLQDGSLNVYYASTSYVLAIGATSQLPSGVTPLVPLWKIPIGLNITNFKTLVYLRSDNTPLQAAYVVGHLKRRTMMFKYDENGTIVDAIDCALDPLSETKCTLRSFIVEKGIYQTSNFRVQPQDTVVRFPNITNLCPFSEVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFQCYGVSSTKLNDLCFTNVYADSFVVRGDEVRQIAPGQTGVIADYNYKLPDDFTGCVLAWNSRNQDASTSGNFNYYYRIWRSEKLRPFERDIAHYDYQVGTQFKSSLKNYGFYSSAGDSHQPYRVVVLSFELLNAPATVCGPKQSTELIKNKCVNFNFNGLTGTGVLTDSNKKFQSFQQFGRDVSDFTDSVKDPKTLEVLDITPCSYGGVSVITPGTNASTQVAVLYQDVNCTDVPTAIHAEQLTPSWRVYSTGTNMFQTQAGCLIGAEHVNNSYDCDIPIGAGICATYHTPSMLRSANNNKRIVAYVMSLGAENSVAYSNNTIAIPTNFTISVTTEVMPVSMTKTSVDCTMYICGDSVECSTLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPDIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFVKQYGDCLGDIQARDLICAQKFNGLTVLPPLLTDEMIAAYTAALISGTATAGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQESLTSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDIISRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYIPSQERNFTTAPAICHEGKAHFPREGVFVSNGTHWFITQRNFYEPQIITTDNTFVSGTCDVVIGIVNNTVYDPLQPELESFKDELDKYFKNHTSPDIDLGDISGINASVVDIQKEIDILKDVAKNLNESLINLQELGKYEQYIGTKHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	9

Entity 3 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	3

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	9

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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	2086299

fit	/app/data/saxs_computation/vg/9vg7/9vg7.fit
pddf	/app/data/pr_computation/vg/9vg7/9vg7.pr.out
profile	/app/data/saxs_computation/vg/9vg7/9vg7.dat

Cryo-EM Structure of Rc-o319 Ectodomain trimer

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