SAXSdb — 9yaz

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1. Structure Basics

entry_id	9yaz
deposition_date	2025-09-16
title	Localized reconstruction of the asymmetric unit of SINV/EEEV in complex with Fab EEEV-179 at 40C sample.
keywords	Eastern Equine Encephalitis Virus, Cryo-EM, Single Particle Averaging, localized reconstruction, asymmetric unit, 40C., VIRUS; VIRUS
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	71.68 Å
rg_electron	71.24 Å
i0	5282200000.00
molecular_weight	611170.0 kDa
excluded_volume	763140 Å³
envelope_volume	1427300 Å³
shell_volume	166420 Å³
envelope_diameter	233.9 Å
shell_rg	73.72 Å
envelope_rg	67.52 Å
shape_rg	71.18 Å
total_rg	71.49 Å
total_atoms	42964
n_residues	5531
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	242.3 Å
rg_real	71.41 Å
rg_real_error	2.55 Å
i0_real	5.2820e+09
i0_real_error	1.1570e+08
rg_reciprocal	72.46 Å
i0_reciprocal	5293000000.0000
total_estimate	0.8765
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	99.1 Å
skewness	0.036
kurtosis	-0.588
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.0000
highest_alpha	253000000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.896

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	EEEV-179 Heavy chain
formula_weight	24245.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1
atom_count	42964

QVQLLQSGAEVKKPGSSVKVSCKASGGTFSNIGISWVRQAPRQGLEWMGGIIPLFATTNYAQNFQGRLTITADKSTTTAYMELNSLRSDDTGVYFCARQLGWAYCNSSTCSKGWFNPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Mesocricetus auratus

Entity 2 polymer

description	EEEV-179 Light chain
formula_weight	23974.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	2

DIVMTQTPLSLPVTPGEPASISCRSSQSLLDSDDGNTYLDWYLQKPGQSPHLLIYTVSYRASGVPDRFSGSGSGTDFTLKISTVEAEDVGVYYCMQRTEFPYTFGQGTKLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Mesocricetus auratus

Entity 3 polymer

description	E1 glycoprotein
formula_weight	47357.5 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E

YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVVKCCGATQCTSKPHPDYQCQVFTGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAKAYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVVYGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQAPSGFERWKRDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDLECKITECTYASDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTANIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWLKVLVGGTSAFIVLGLIATAVVALVLF

Source

organism	Eastern equine encephalitis virus
ncbi_taxonomy_id	11021
host_organism	Mesocricetus auratus

Entity 4 polymer

description	Capsid protein
formula_weight	17650.0 kDa
ec_number	3.4.21.90
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	P,Q,R,S,T

QRMCMKLESDKTFPIMLNGQVNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCMKSDTLQYTSDKPPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGGVNEGSRTALSVVTWNQKGVTVKDTPEGSEPW

Source

organism	Eastern equine encephalitis virus
ncbi_taxonomy_id	11021
host_organism	Mesocricetus auratus

Entity 5 polymer

description	E2 glycocprotein
formula_weight	47047.0 kDa
ec_number	3.4.21.90
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	a,b,c,d,e

DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGVDLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRHTCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSIHSAKVKITVPSGAQVKYYCKCPDVREGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRLPRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSDANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRYPLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTRA

Source

organism	Eastern equine encephalitis virus
ncbi_taxonomy_id	11021
host_organism	Mesocricetus auratus

Entity 6 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	4

Entity 7 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	—

resolution	3.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.80 Å
resolution_method	—
num_particles	2225480

fit	/app/data/saxs_computation/ya/9yaz/9yaz.fit
pddf	/app/data/pr_computation/ya/9yaz/9yaz.pr.out
profile	/app/data/saxs_computation/ya/9yaz/9yaz.dat

Localized reconstruction of the asymmetric unit of SINV/EEEV in complex with Fab EEEV-179 at 40C sample.

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

Refinement

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 branched

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)