SAXSdb — 9yka

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1. Structure Basics

entry_id	9yka
deposition_date	2025-10-06
title	Cryo-EM structure of post-fusion EBV gB in complex with AMMO2 fab
keywords	Post-fusion, AMMO2, fab, 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	39.96 Å
rg_electron	39.44 Å
i0	393297000.00
molecular_weight	158620.0 kDa
excluded_volume	197210 Å³
envelope_volume	267210 Å³
shell_volume	58028 Å³
envelope_diameter	129.8 Å
shell_rg	43.98 Å
envelope_rg	39.02 Å
shape_rg	39.46 Å
total_rg	39.65 Å
total_atoms	11157
n_residues	1380
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	127.0 Å
rg_real	39.79 Å
rg_real_error	1.13 Å
i0_real	3.9330e+08
i0_real_error	6.4510e+06
rg_reciprocal	39.90 Å
i0_reciprocal	393300000.0000
total_estimate	0.9056
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	50.8 Å
skewness	0.145
kurtosis	-0.579
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	25910000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.927

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	AMMO2 fab heavy chain
formula_weight	14393.0 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	F,H,D
atom_count	11157

QVQLVQSGAEVKKPGSSIKVSCKTSGGPFSTYGINWVRQAPGQGLEWMGWIIPVFDTSSFAQRFQDRLSITADASTSTAYMELRSLRSEDTAVYYCARDRVLGAHGANPLNGHHYGMDVWGQGTTVTVSSAST

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	AMMO2 fab light chain
formula_weight	23134.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,I,E

DIQITQSPSSVSASVGDRVTITCRANLGISDWLAWYQQKPGRAPKLLIYAASSLESGVPSRFSGSGSGIYFTLTISSLQPEDVATYFCQQANSFPLSFGGGTRVDIARTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	BALF4
formula_weight	81665.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C

MTRRRVLSVVVLLAALACRLGAQTPEQPAPPATTVQPTATRQQTSFPFRVCELSSHGDLFRFSSDIQCPSFGTRENHTEGLLMVFKDNIIPYSFKVRSYTKIVTNILIYNGHRADSVTNRHEEKFSVESYETDQMDTIYQCYNAVKMTKDGLTRVYVDRDGVNITVNLKPTGGLANGVRRYASQTELYDAPGRVEATYRTRTTVNCLITDMMAKSNSPFEFFVTTTGQTVEMSPFYDGKNTETFHERADSFHVRTNYKIVDYDNRGTNPQGERRAFLDKGTYTLSWKLENRTAYCPLQHWQTFDSTIATETGKSIHFVTDEGTSSFVTNTTVGIELPDAFKCIEEQVNKTMHEKYEAVQDRYTKGQEAITYFITSGGLLLAWLPLTPRSLATVKNLTELTTPTSSPPSSPSPPAPPAARGSTSAAVLGGSGGNAGNATTPVPPAAPGKSLGTLNNPATVQIQFAYDSLRRQINRMLGDLARAWCLEQKRQNMVLRELTKINPTTVMSSIYGKAVAAKRLGDVISVSQCVPVNQATVTLRKSMRVPGSETMCYSRPLVSFSFINDTKTYEGQLGTDNEIFLTKKMTEVCQATSQYYFQSGNEIHVYNDYHHFKTIELDGIATLQTFISLNTSLIENIDFASLELYSRDEQRASNVFDLEGIFREYNFQAQNIAGLRKDLDNAVSNGRNQGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRAAASSLEVLFQGPG

Source

organism	human gammaherpesvirus 4
common_name	Epstein-Barr virus
ncbi_taxonomy_id	10376
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

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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	triclinic

resolution	2.90 Å
resolution_method	—
num_particles	154000

fit	/app/data/saxs_computation/yk/9yka/9yka.fit
pddf	/app/data/pr_computation/yk/9yka/9yka.pr.out
profile	/app/data/saxs_computation/yk/9yka/9yka.dat

Cryo-EM structure of post-fusion EBV gB in complex with AMMO2 fab

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)