SAXSdb — 9s6r

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1. Structure Basics

entry_id	9s6r
deposition_date	2025-08-01
title	Ternary cryo-EM structure of yeast ALG3 with Dol25-PP-GlcNAc2Man5, Dol25-P-Man, and Fab
keywords	Mannosyltransferase, ternary complex, N-linked glycosylation, 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	30.42 Å
rg_electron	30.08 Å
i0	147722000.00
molecular_weight	67297.0 kDa
excluded_volume	66527 Å³
envelope_volume	111110 Å³
shell_volume	31859 Å³
envelope_diameter	110.6 Å
shell_rg	36.14 Å
envelope_rg	30.27 Å
shape_rg	30.10 Å
total_rg	30.45 Å
total_atoms	5104
n_residues	618
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	105.4 Å
rg_real	30.56 Å
rg_real_error	0.80 Å
i0_real	1.4770e+08
i0_real_error	2.4410e+06
rg_reciprocal	30.51 Å
i0_reciprocal	147700000.0000
total_estimate	0.6646
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	30.4 Å
skewness	0.414
kurtosis	-0.528
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	14810000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.803; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Sc-16 Fab heavy chain
formula_weight	25714.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	5114

EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSSSSIHWVRQAPGKGLEWVASISSSSGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSQKMSYWWWYFYHYWPAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	Sc-16 Fab light chain
formula_weight	23258.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 polymer

description	Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase
formula_weight	53925.9 kDa
ec_number	2.4.1.258
mutation	D71N
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MEGEQSPQGEKSLQRKQFVRPPLDLWQDLKDGVRYVIFDCRANLIVMPLLILFESMLCKIIIKKVAYTEINYKAYMEQIEMIQLDGMLDYSQVSGGTGPLVYPAGHVLIYKMMYWLTEGMDHVERGQVFFRYLYLLTLALQMACYYLLHLPPWCVVLACLSKRLHSIYVLRLFNDCFTTLFMVVTVLGAIVASRCHQRPKLKKSLALVISATYSMAVSIKMNALLYFPAMMISLFILNDANVILTLLDLVAMIAWQVAVAVPFLRSFPQQYLHCAFNFGRKFMYQWSINWQMMDEEAFNDKRFHLALLISHLIALTTLFVTRYPRILPDLWSSLCHPLRKNAVLNANPAKTIPFVLIASNFIGVLFSRSLHYQFLSWYHWTLPILIFWSGMPFFVGPIWYVLHEWCWNSYPPNSQASTLLLALNTVLLLLLALTQLSGSVALAKSHLRTTSSMEKKLNVDALEVLFQ

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Homo sapiens

Entity 4 non-polymer

description	;[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-5-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{S},4~{S},5~{R},6~{R})-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,5-bis(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-2-yl]oxy-6-(hydroxymethyl)-4-oxidanyl-oxan-2-yl] [oxidanyl-[(3~{S},6~{Z},10~{E},14~{E})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphoryl] hydrogen phosphate ;
formula_weight	1575.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CHOLESTEROL HEMISUCCINATE
formula_weight	486.7 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	Dolichol monophosphate beta-D-Mannose
formula_weight	602.7 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	10

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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	triclinic

resolution	3.08 Å
resolution_method	—
num_particles	243185

fit	/app/data/saxs_computation/s6/9s6r/9s6r.fit
pddf	/app/data/pr_computation/s6/9s6r/9s6r.pr.out
profile	/app/data/saxs_computation/s6/9s6r/9s6r.dat

Ternary cryo-EM structure of yeast ALG3 with Dol25-PP-GlcNAc2Man5, Dol25-P-Man, and Fab

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

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)