SAXSdb — 9rdt

▼

1. Structure Basics

entry_id	9rdt
deposition_date	2025-06-03
last_revision	2025-09-24
title	Structure of the RhGB07 Prefusion, Closed-state trimeric spike protein
keywords	Spike protein of RhGB07 coronavirus, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	51.42 Å
rg_electron	51.03 Å
i0	2130090000.00
molecular_weight	385770.0 kDa
excluded_volume	482390 Å³
envelope_volume	715200 Å³
shell_volume	113360 Å³
envelope_diameter	170.0 Å
shell_rg	56.84 Å
envelope_rg	50.68 Å
shape_rg	51.04 Å
total_rg	51.19 Å
total_atoms	27117
n_residues	3273
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	169.9 Å
rg_real	51.36 Å
rg_real_error	1.53 Å
i0_real	2.1300e+09
i0_real_error	3.8820e+07
rg_reciprocal	51.46 Å
i0_reciprocal	2130000000.0000
total_estimate	0.8657
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.3 Å
skewness	0.335
kurtosis	-0.337
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	431500000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.710

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	RhGB07 Spike- T4 foldon fusion protein
formula_weight	138592.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,B,A
atom_count	27117

DGCGRLSQKTQPKLEQFNSSRRGLYYFDDIFRSSLRVLTSGYFLPFGSNVTRYEVKQVPQVPIYYDNPLVPFGHGVYFAVTEKSNVVRGWIFGSTMDNTTQSAVLVNNGTHIVVNVCNFNFCADPMFAVSAGQSYKSWIYTSSTNCTYFQAFPFAIETRPNGTGPFTHLREHVFRNVDGFLHVYHNYEVINVQNGLPSGFSVLRPIFKLPLGLNITYIKAVMTLFSSTTSNFIAAVASLHYVGYLQPRTMLFHFDQNGTIVDAIDCSQNPLSELKCTTKSFSLEKGIYQTSNFRVTPTTEVIRFPNVTQLCPFSDVFNRTKFPSVYAWERMSIRDCVADYAVLYNSSISFSTFECYGVSPTKLNDLCFSSVYADYFVVRGDDVKQIAPGKTGVIADYNYKLPDDFVGCVLAWNSRHVDSKQGFYYRLFRHGKIKPYQRDMSRELYSPSGTPCTTEGFNCYDPLAHYAFASPGIGTGYQPFRVVVLSFQLLNAPATVCGPKQSTDLVKNKCVNFNFNGLTGTGVLTDSVKKFQPFQQFGRDSSDFTDSVKDPKTLEILDITPCSYGGVSVITPGTNTSDAVAVLYQDVNCTDVPTMLHIDQVSSDWRVYAANTGGNMFQTQAGCLVGATYDNTSYECDIPVGAGVCAKFQINTGASQSSILAYTMSLGEDSNVAYSNNSIAIPTNFSISVTTEVLPVSMTKTSVDCNMYICGDSTECSSLLLQYGSFCQQLNRALAGVSVEQDKNTQDVFAQVKSIYKVPAIKDFGGFNFSHILPDPAKPSKRSFIEDLLYNKVTLADPGFMKQYGDCLGGVNARDLICAQKFNGLTVLPPLLTDDMIAAYTSALVSGTALSGYTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTATALGKLQDVINQNAIALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQEQNFTTAPAICHKGKAHFPREGVFVTNGTHWFVTQRNFYQPEVITTENTFESGNCDVVIGIVNNTVYDPLQPELESFKEELDKYFKNHTSPEVGFDDISGINASVVDIKKEIAHLNEIASKLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK

Source

organism	Sarbecovirus sp. RhGB07
ncbi_taxonomy_id	3030542
host_organism	Cricetulus griseus

Entity 2 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	383.3 kDa
src_method	man
entity_count	3

Entity 3 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	21

Entity 4 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	15

Entity 5 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	3

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	18

▶

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	triclinic

resolution	2.97 Å
resolution_method	—
num_particles	17685

fit	/app/data/saxs_computation/rd/9rdt/9rdt.fit
pddf	/app/data/pr_computation/rd/9rdt/9rdt.pr.out
profile	/app/data/saxs_computation/rd/9rdt/9rdt.dat

Structure of the RhGB07 Prefusion, Closed-state trimeric spike protein

SAXS Profile

P(r) Distribution