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9uoc

Crystal structure of nanobody Tnb150 with MERS-CoV RBD

Method: X-RAY DIFFRACTION D_max: 126.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uoc
deposition_date	2025-04-25
last_revision	2026-04-29
title	Crystal structure of nanobody Tnb150 with MERS-CoV RBD
keywords	MERS-CoV, nanobody, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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	38.07 Å
rg_electron	37.81 Å
i0	318910000.00
molecular_weight	144170.0 kDa
excluded_volume	179900 Å³
envelope_volume	234780 Å³
shell_volume	52548 Å³
envelope_diameter	135.7 Å
shell_rg	42.96 Å
envelope_rg	37.43 Å
shape_rg	37.78 Å
total_rg	38.22 Å
total_atoms	10110
n_residues	1313
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	126.5 Å
rg_real	38.20 Å
rg_real_error	0.85 Å
i0_real	3.1890e+08
i0_real_error	5.0490e+06
rg_reciprocal	38.12 Å
i0_reciprocal	318900000.0000
total_estimate	0.8684
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.1 Å
skewness	0.429
kurtosis	-0.404
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	53580000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.827

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Spike glycoprotein
formula_weight	22930.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,C,E,G
atom_count	10110

VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKL

Source

organism	Middle East respiratory syndrome-related coronavirus
ncbi_taxonomy_id	1335626
host_organism	Trichoplusia ni

Entity 2 polymer

description	Tnb150
formula_weight	13227.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,D,F,H

QLVESGGGLAQPGGSLRLSCGGSMIPFDRYFIGWFRQAPGKEREAISCISTDGDSTNYADSVKGRFTMSRDNPGNTVYLQMNSLKPEDTAVYYCAAHLTSVQAMCLLSTVGYWGQGTQVTVSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

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	80.926 Å
length_b	116.604 Å
length_c	87.058 Å
angle_alpha	90.00 °
angle_beta	93.34 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	3.240 Å
resolution_low	86.910 Å
r_factor	0.2905
r_work	0.2869
r_free	0.3316

fit	/app/data/saxs_computation/uo/9uoc/9uoc.fit
pddf	/app/data/pr_computation/uo/9uoc/9uoc.pr.out
profile	/app/data/saxs_computation/uo/9uoc/9uoc.dat

Crystal structure of nanobody Tnb150 with MERS-CoV RBD

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)