;SARS-CoV-2 S2 trimer stabilized in the early fusion intermediate conformation by circular permutation and clamping by gp41 (E-FICs-v1) ;

Method: ELECTRON MICROSCOPY D_max: 245.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z3k
deposition_date	2025-11-07
title	;SARS-CoV-2 S2 trimer stabilized in the early fusion intermediate conformation by circular permutation and clamping by gp41 (E-FICs-v1) ;
keywords	;S2prime, coronavirus, SARS-CoV-2, spike, fusion, entry, antiviral, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, 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	82.38 Å
rg_electron	84.33 Å
i0	212038000.00
molecular_weight	119080.0 kDa
excluded_volume	147640 Å³
envelope_volume	252470 Å³
shell_volume	32015 Å³
envelope_diameter	277.1 Å
shell_rg	47.90 Å
envelope_rg	86.46 Å
shape_rg	84.58 Å
total_rg	82.53 Å
total_atoms	8448
n_residues	1212
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	245.2 Å
rg_real	82.30 Å
rg_real_error	2.30 Å
i0_real	2.1000e+08
i0_real_error	4.8930e+06
rg_reciprocal	73.55 Å
i0_reciprocal	207100000.0000
total_estimate	0.6016
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	38.7 Å
skewness	0.558
kurtosis	-0.954
angular_range	— – 0.0950 Å⁻¹
current_alpha	0.0199
highest_alpha	5473000.0000
n_real_points	20
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.018; Stabil: 0.948; Sysdev: 1.000; Positv: 1.000; Valcen: 0.007; Smooth: 0.846

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4. Crystallography & Experiment

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5. Entities & Polymer Info (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	3.30 Å
resolution_method	—
num_particles	114104

description	SPIKE PROTEIN
formula_weight	68016.2 kDa
src_method	man
entity_count	3

type	polypeptide(L)
strand_id	A,B,C
atom_count	8448

;SARS-CoV-2 S2 trimer stabilized in the early fusion intermediate conformation by circular permutation and clamping by gp41 (E-FICs-v1) ;

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Homo sapiens

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

fit	/app/data/saxs_computation/z3/9z3k/9z3k.fit
pddf	/app/data/pr_computation/z3/9z3k/9z3k.pr.out
profile	/app/data/saxs_computation/z3/9z3k/9z3k.dat