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11hk

;SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to the VN01H1 Fab (Fab local refinement) ;

Method: ELECTRON MICROSCOPY D_max: 153.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11hk
deposition_date	2026-02-24
title	;SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to the VN01H1 Fab (Fab local refinement) ;
keywords	;S2prime, coronavirus, SARS-CoV-2, spike, fusion, entry, antiviral, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, VIRAL PROTEIN-HYDROLASE complex, VN01H1, 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	40.12 Å
rg_electron	39.95 Å
i0	252060000.00
molecular_weight	129840.0 kDa
excluded_volume	162770 Å³
envelope_volume	212160 Å³
shell_volume	47084 Å³
envelope_diameter	161.4 Å
shell_rg	41.90 Å
envelope_rg	40.45 Å
shape_rg	39.95 Å
total_rg	40.07 Å
total_atoms	9204
n_residues	1254
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	153.3 Å
rg_real	40.29 Å
rg_real_error	2.18 Å
i0_real	2.5210e+08
i0_real_error	4.8220e+06
rg_reciprocal	40.12 Å
i0_reciprocal	252000000.0000
total_estimate	0.8157
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	51.1 Å
skewness	0.556
kurtosis	0.420
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	16770000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.613; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.827; Smooth: 0.933

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	E-FICS-v3
formula_weight	67787.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,D,G
atom_count	9288

MTRLTVLALLAGLLASSRASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRENDDDDKTGTGSQSNAESVQNHTFEVLNNTIRALELILRKLEILYEMILQLHEEVEAIQKAINVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLAKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGTNSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFTIDKEKWKEWRKEMENLTKEIKETLEEARKTLKQAEETFKTPSSGGTDDDDKTGSLNDIFEAQKIEWHEQGSHHHHHHHH

Source

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

Entity 2 polymer

description	Heavy chain of VN01H1 Fab
formula_weight	24131.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,E,H

EVQLVESGGGLVLPGGSLRLSCSASGFTFSDFSMHWVRQSPGKGLEYVSAITSSGSSTYYPDSVKGRFTISRDNSKNTLYLQMGSLRVEDTAVYWCVKNSDVFRFPHLYFDVWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Light chain of VN01H1 Fab
formula_weight	23413.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,F,I

DIVMTQSPATLSVSPGDRATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRAAGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYDNWPSITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	6

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	84

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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	2.70 Å
resolution_method	—
num_particles	121952

fit	/app/data/saxs_computation/1h/11hk/11hk.fit
pddf	/app/data/pr_computation/1h/11hk/11hk.pr.out
profile	/app/data/saxs_computation/1h/11hk/11hk.dat

;SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to the VN01H1 Fab (Fab local refinement) ;

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)