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9ub6

Crystal structure of SFTSV Gn head with nanobody Nb261

Method: X-RAY DIFFRACTION D_max: 85.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ub6
deposition_date	2025-04-02
title	Crystal structure of SFTSV Gn head with nanobody Nb261
keywords	SFTSV, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

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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	25.14 Å
rg_electron	24.24 Å
i0	41081700.00
molecular_weight	47893.0 kDa
excluded_volume	59193 Å³
envelope_volume	70552 Å³
shell_volume	25047 Å³
envelope_diameter	89.1 Å
shell_rg	30.72 Å
envelope_rg	24.53 Å
shape_rg	24.17 Å
total_rg	25.15 Å
total_atoms	3350
n_residues	425
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	85.5 Å
rg_real	25.21 Å
rg_real_error	0.66 Å
i0_real	4.1080e+07
i0_real_error	6.1570e+05
rg_reciprocal	25.19 Å
i0_reciprocal	41080000.0000
total_estimate	0.8758
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.1 Å
skewness	0.443
kurtosis	-0.192
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	8352000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.897; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glycoprotein N
formula_weight	35050.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3350

GPIICAGPIHSNKSADIPHLLGYSEKICQIDRLIHVSSWLRNHSQFQGYVGQRGGRSQVSYYPAENSYSRWSGLLSPCDADWLGMLVVKKAKGSDMIVPGPSYKGKVFFERPTFDGYVGWGCGSGKSRTESGELCSSDSGTSSGLLPSDRVLWIGDVACQPMTPIPEETFLELKSFSQSEFPDICKIDGIVFNQCEGESLPQPFDVAWMDVGHSHKIIMREHKTKWVQESSSKDFVCYKEGTGPCSESEEKTCKTSGSCRGDMQFCKVAGCEHGEEASEAKCRCSLVHKPGEVVVSYGGMRVRPKCYGFSRMMATLEV

Source

organism	SFTS virus HB29
ncbi_taxonomy_id	992212
host_organism	Baculovirus expression vector pFastBac1-HM

Entity 2 polymer

description	Nanobody VHH261
formula_weight	12623.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

AVQLVESGGGLVQPGGSLRLSCAASGFTISNADMRWYRQAPGKERELVALLLSSLGGSTEYADSVKGRFTMFRDNARNTVYLQMDNLKAEDTAVYYCNVRWTDYWGQGTQVTVSS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Mammalian expression vector pCAGGS

Entity 3 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	1

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	172.710 Å
length_b	172.710 Å
length_c	136.030 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 62 2 2
int_tables_number	180
crystal_system	hexagonal

resolution	2.890 Å
resolution_low	52.200 Å
r_factor	0.1933
r_work	0.1912
r_free	0.2213

fit	/app/data/saxs_computation/ub/9ub6/9ub6.fit
pddf	/app/data/pr_computation/ub/9ub6/9ub6.pr.out
profile	/app/data/saxs_computation/ub/9ub6/9ub6.dat

Crystal structure of SFTSV Gn head with nanobody Nb261

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

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)