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9znn

;Cryo-EM structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) in complex with APPB ;

Method: ELECTRON MICROSCOPY D_max: 101.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9znn
deposition_date	2025-12-14
title	;Cryo-EM structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) in complex with APPB ;
keywords	polyprenyl-phosphate N-acetylhexosamine phosphate transferase, phosphoglycosyltransferase, membrane protein, TRANSFERASE; TRANSFERASE
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	29.86 Å
rg_electron	29.15 Å
i0	215493000.00
molecular_weight	83359.0 kDa
excluded_volume	83320 Å³
envelope_volume	138170 Å³
shell_volume	39168 Å³
envelope_diameter	107.2 Å
shell_rg	36.81 Å
envelope_rg	29.89 Å
shape_rg	29.14 Å
total_rg	29.67 Å
total_atoms	6351
n_residues	771
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	101.5 Å
rg_real	29.87 Å
rg_real_error	0.78 Å
i0_real	2.1550e+08
i0_real_error	3.5440e+06
rg_reciprocal	29.87 Å
i0_reciprocal	215500000.0000
total_estimate	0.8755
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.5 Å
skewness	0.393
kurtosis	-0.252
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	28490000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.938

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
formula_weight	47312.9 kDa
ec_number	2.7.8.15
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6462

MWAFSELPMPLLINLIVSLLGFVATVTLIPAFRGHFIAARLCGQDLNKTSRQQIPESQGVISGAVFLIILFCFIPFPFLNCFVKEQCKAFPHHEFVALIGALLAICCMIFLGFADDVLNLRWRHKLLLPTAASLPLLMVYFTNFGNTTIVVPKPFRPILGLHLDLGILYYVYMGLLAVFCTNAINILAGINGLEAGQSLVISASIIVFNLVELEGDCRDDHVFSLYFMIPFFFTTLGLLYHNWYPSRVFVGDTFCYFAGMTFAVVGILGHFSKTMLLFFMPQVFNFLYSLPQLLHIIPCPRHRIPRLNIKTGKLEMSYSKFKTKSLSFLGTFILKVAESLQLVTVHQSETEDGEFTECNNMTLINLLLKVLGPIHERNLTLLLLLLQILGSAITFSIRYQLVRLFYDVGSSASENLYFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	;4-({(2S,3S)-1-amino-3-{[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxyoxolan-2-yl]oxy}-3-[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]-1-oxopropan-2-yl}amino)-N-[(4-{4-[4-(trifluoromethoxy)phenoxy]piperidin-1-yl}phenyl)methyl]butanamide (non-preferred name) ;
formula_weight	881.8 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	(2R)-3-{[(S)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(9Z)-octadec-9-enoyl]oxy}propyl (9Z)-octadec-9-enoate
formula_weight	775.0 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	80

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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	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	82209

fit	/app/data/saxs_computation/zn/9znn/9znn.fit
pddf	/app/data/pr_computation/zn/9znn/9znn.pr.out
profile	/app/data/saxs_computation/zn/9znn/9znn.dat

;Cryo-EM structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) in complex with APPB ;

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