SAXSdb — 9yb4

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1. Structure Basics

entry_id	9yb4
deposition_date	2025-09-16
title	Localized reconstruction of the asymmetric unit of the low pH treated back neutralized SINV/EEEV.
keywords	;Eastern Equine Encephalitis Virus, Cryo-EM, Single Particle Averaging, localized reconstruction, asymmetric unit, low pH back neutralization., 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	65.65 Å
rg_electron	65.14 Å
i0	2916680000.00
molecular_weight	452590.0 kDa
excluded_volume	565200 Å³
envelope_volume	988630 Å³
shell_volume	127300 Å³
envelope_diameter	211.1 Å
shell_rg	67.66 Å
envelope_rg	61.76 Å
shape_rg	65.08 Å
total_rg	65.40 Å
total_atoms	31820
n_residues	4078
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	209.9 Å
rg_real	65.32 Å
rg_real_error	2.67 Å
i0_real	2.9170e+09
i0_real_error	6.4680e+07
rg_reciprocal	65.88 Å
i0_reciprocal	2919000000.0000
total_estimate	0.8770
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	87.4 Å
skewness	0.082
kurtosis	-0.621
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0000
highest_alpha	127600000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.574

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	E1 glycoprotein
formula_weight	47938.1 kDa
ec_number	3.4.21.90
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	31820

YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVVKCCGATQCTSKPHPDYQCQVFTGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAKAYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVVYGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQAPSGFERWKRDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDLECKITECTYASDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTANIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWLKVLVGGTSAFIVLGLIATAVVALVLFFHRH

Source

organism	Eastern equine encephalitis virus
ncbi_taxonomy_id	11021
host_organism	Mesocricetus auratus

Entity 2 polymer

description	Capsid protein
formula_weight	17650.0 kDa
src_method	man
entity_count	4

Polymer

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

QRMCMKLESDKTFPIMLNGQVNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCMKSDTLQYTSDKPPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGGVNEGSRTALSVVTWNQKGVTVKDTPEGSEPW

Source

organism	Eastern equine encephalitis virus
ncbi_taxonomy_id	11021
host_organism	Mesocricetus auratus

Entity 3 polymer

description	E2 glycoprotein
formula_weight	46860.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	a,d

LDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGVDLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRHTCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSIHSAKVKITVPSGAQVKYYCKCPDVREGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRLPRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSDANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRYPLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTR

Source

organism	Eastern equine encephalitis virus
ncbi_taxonomy_id	11021
host_organism	Mesocricetus auratus

Entity 4 polymer

description	E2 glycoprotein
formula_weight	46975.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	b,c

DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGVDLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRHTCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSIHSAKVKITVPSGAQVKYYCKCPDVREGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRLPRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSDANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRYPLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTR

Source

organism	Eastern equine encephalitis virus
ncbi_taxonomy_id	11021
host_organism	Mesocricetus auratus

Entity 5 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 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	4

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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	3.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.10 Å
resolution_method	—
num_particles	958879

fit	/app/data/saxs_computation/yb/9yb4/9yb4.fit
pddf	/app/data/pr_computation/yb/9yb4/9yb4.pr.out
profile	/app/data/saxs_computation/yb/9yb4/9yb4.dat

Localized reconstruction of the asymmetric unit of the low pH treated back neutralized SINV/EEEV.

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)