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9ucl

CryoEM structure of IgV domain of human Nectin-4 with Trimbody

Method: ELECTRON MICROSCOPY D_max: 141.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ucl
deposition_date	2025-04-04
title	CryoEM structure of IgV domain of human Nectin-4 with Trimbody
keywords	STRUCTURAL PROTEIN; STRUCTURAL 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	45.19 Å
rg_electron	44.62 Å
i0	684089000.00
molecular_weight	220630.0 kDa
excluded_volume	278410 Å³
envelope_volume	386920 Å³
shell_volume	72579 Å³
envelope_diameter	146.0 Å
shell_rg	49.67 Å
envelope_rg	43.64 Å
shape_rg	44.66 Å
total_rg	44.69 Å
total_atoms	15549
n_residues	2031
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	141.2 Å
rg_real	44.93 Å
rg_real_error	0.87 Å
i0_real	6.8410e+08
i0_real_error	1.0230e+07
rg_reciprocal	45.19 Å
i0_reciprocal	684300000.0000
total_estimate	0.8923
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	60.5 Å
skewness	0.057
kurtosis	-0.516
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	36840000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.842

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
formula_weight	36127.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	15549

MKEIAKIVAELLRGIARIIDDIKGRDREEEVEILAKAVEKTGKPEDVRLALEAAERGVTLDQAKAIAQILSMPNLTDEQKRGFVQSLLDDPSVSKEILAEAKKLNEHQAAKAEEAARKMEELFKKHKIVAVLRANSVEEAIEKAVAVFAGGVHLIEITFTVPDADTVIKALSVLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGCTEAAALEHHHHHH

Source

organism	Thermotoga maritima MSB8
ncbi_taxonomy_id	243274
host_organism	Escherichia coli

Entity 2 polymer

description	N4-nanobody-TAIL
formula_weight	27671.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

MAEVQLQASGGGFVQPGGSLRLSCAASGRFSAFYNMGWFRQAPGKEREFVSAISWSTNSAAYYADSVKGRFTISRDNSKNTVYLQMNSLRAEDTATYYCAASWHWNPPDHSWDAGYWGQGTLVAVVKTVEDAFLALLALEQHLGVQPADLAALAEKLNLSQLLELGELLKAAGHPLAPQVEALLKEKLKAASAAEAAGVIFQALVKDEELGKKILEWAKEFGTEEAKKAIEIAEKAYELYKKYLEHHHHHH

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 polymer

description	Nectin-4
formula_weight	13566.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,H,I

MGELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLEHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

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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	2.430 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.43 Å
resolution_method	—
num_particles	567049

fit	/app/data/saxs_computation/uc/9ucl/9ucl.fit
pddf	/app/data/pr_computation/uc/9ucl/9ucl.pr.out
profile	/app/data/saxs_computation/uc/9ucl/9ucl.dat

CryoEM structure of IgV domain of human Nectin-4 with Trimbody

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)