SAXSdb — 9x3j

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1. Structure Basics

entry_id	9x3j
deposition_date	2025-10-09
title	Glycoprotein of Mengla Virus with MR191 Fab bound
keywords	Mengla Virus Glycoprotein, 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	42.81 Å
rg_electron	42.17 Å
i0	402754000.00
molecular_weight	165850.0 kDa
excluded_volume	208230 Å³
envelope_volume	287740 Å³
shell_volume	57255 Å³
envelope_diameter	137.4 Å
shell_rg	47.06 Å
envelope_rg	41.37 Å
shape_rg	42.15 Å
total_rg	42.50 Å
total_atoms	11679
n_residues	1464
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	134.8 Å
rg_real	42.66 Å
rg_real_error	1.05 Å
i0_real	4.0280e+08
i0_real_error	6.7450e+06
rg_reciprocal	42.81 Å
i0_reciprocal	402800000.0000
total_estimate	0.8999
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	61.9 Å
skewness	0.047
kurtosis	-0.737
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	41540000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.894

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Envelope glycoprotein
formula_weight	73748.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,E
atom_count	11679

MALAKKYLMRIFIISHYFLSYNYGFFLPIVKLDIQPENEIIKSPCNGVVKKTEDIHLMSLTLTGQKTASDPMAASKRWAFKEGVLPKTVAFTEGEEAKDCFNISIVDLQGRSLLLEAPSGIKDYPRCKSIHHIQGQNPHAKGNVLHLWGAFFLYDRIASTTMFKDKVFAEGNVAALVINKTVHHQIFKINKIPQNETIGSCNHTYWRSDAGDGFNTTLAVTNLAYVLSANESTKIFKQMQDDLRKRIENMTSSNLTTLSPEAISNSSDANSSATIAYGTSGASISATTRSATSTLTITTDGQMSPPPTPAPPSPSLKPSTDDIKTPTVLSTTSSSTRSKRSVTVAKQSSANPTGKQRGRGRKGPSTGTLTEEQIERVRMLIQKNVGRVNYNNLPLIAGLTALKKKRQVLETFSGEIELEELIGDEKLDSRFRENLKMILETLRNESYSHFELDIPKTAALKSPEETDPRIHMEYLGSGEEPIQSNGQTDTDCDPSLRIWTPNEEKLAAGVSWIPYFGPGAEGLYTMGLMQNQNDVVCRLRRLANQTAKSLDLLLRVTTEERTYSIINRHAIDFLLARWGGTCRVLGPECCIGVEDLTKNITDQIQQMRRDEQDEYEGWGKGGNWFNSQFGNWLNLGILIFLFLGIIIALSCVCRLFMNLTVY

Source

organism	Dianlovirus menglaense
ncbi_taxonomy_id	3052181
host_organism	Homo sapiens

Entity 2 polymer

description	MR191 Fab Heavy Chain
formula_weight	24490.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	I,C,F

QLQLQESGPGLVKPSETLSLSCTVSGVSISDNSYYWGWIRQPPGKGLEWIGTISYSGNTYYNPSLKSRVSISGDTSKHQLSLKVSSVTAADTAVYYCARQRIVSGFVEWLSKFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	MR191 Fab Light Chain
formula_weight	22894.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	M,D,G

QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGFDVHWYQQLPGTAPKLLIYDNNNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDTSLSGPVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1073.0 kDa
src_method	man
entity_count	3

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	3

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

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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	3.470 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.47 Å
resolution_method	—
num_particles	15563

fit	/app/data/saxs_computation/x3/9x3j/9x3j.fit
pddf	/app/data/pr_computation/x3/9x3j/9x3j.pr.out
profile	/app/data/saxs_computation/x3/9x3j/9x3j.dat

Glycoprotein of Mengla Virus with MR191 Fab bound

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 branched

Entity 5 branched

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)