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9vls

;Cryo-EM structure of SARS-CoV-2 XBB.1.5 S trimer in the early fusion intermediate conformation (E-FIC) complexed with ACE2 and 76E1-Fab (focused refinement of the S2-76E1) ;

Method: ELECTRON MICROSCOPY D_max: 221.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vls
deposition_date	2025-06-26
title	;Cryo-EM structure of SARS-CoV-2 XBB.1.5 S trimer in the early fusion intermediate conformation (E-FIC) complexed with ACE2 and 76E1-Fab (focused refinement of the S2-76E1) ;
keywords	Spike, ACE2, and 76E1-Fab complex, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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	75.10 Å
rg_electron	76.02 Å
i0	1088890000.00
molecular_weight	278280.0 kDa
excluded_volume	348340 Å³
envelope_volume	575860 Å³
shell_volume	69448 Å³
envelope_diameter	246.1 Å
shell_rg	60.82 Å
envelope_rg	75.94 Å
shape_rg	76.03 Å
total_rg	75.69 Å
total_atoms	19572
n_residues	2559
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	221.4 Å
rg_real	75.72 Å
rg_real_error	1.87 Å
i0_real	1.0880e+09
i0_real_error	2.1090e+07
rg_reciprocal	72.07 Å
i0_reciprocal	1080000000.0000
total_estimate	0.7549
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	52.7 Å
skewness	0.431
kurtosis	-0.915
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.0019
highest_alpha	32360000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.728; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.626; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Spike glycoprotein
formula_weight	142392.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	19572

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPVDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSHHHHHHHH

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV, SARS-CoV-2
ncbi_taxonomy_id	2697049
host_organism	Homo sapiens

Entity 2 polymer

description	heavy chain of 76E1 Fab
formula_weight	23378.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,I,K

EVQLVESGGGVVQPGGSLRLSCEASGFSFKDYGMHWIRQTPGKGLEWISRISGDTRGTSYVDSVKGRFIVSRDNSRNSLFLQMNSLRSEDTALYYCAALVIVAAGDDFDLWGQGTVVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	light chain of 76E1 Fab
formula_weight	22949.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,J,L

QSALTQPLSVSGSPGQSVTISCTGSSSDIGSYNFVSWYRQYPGKAPKVMIYEVNKRPSGVPVRFSGSKSGNTASLTVSGLQHEDEADYYCCSYGGRNNLIFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
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	12

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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	4.14 Å
resolution_method	—
num_particles	39788

fit	/app/data/saxs_computation/vl/9vls/9vls.fit
pddf	/app/data/pr_computation/vl/9vls/9vls.pr.out
profile	/app/data/saxs_computation/vl/9vls/9vls.dat

;Cryo-EM structure of SARS-CoV-2 XBB.1.5 S trimer in the early fusion intermediate conformation (E-FIC) complexed with ACE2 and 76E1-Fab (focused refinement of the S2-76E1) ;

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)