SAXSdb — 9s6s

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1. Structure Basics

entry_id	9s6s
deposition_date	2025-08-01
title	Ternary cryo-EM structure of human ALG9 with Dol25-PP-GlcNAc2Man6, 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	35.98 Å
rg_electron	35.72 Å
i0	224828000.00
molecular_weight	84579.0 kDa
excluded_volume	83925 Å³
envelope_volume	148380 Å³
shell_volume	37449 Å³
envelope_diameter	134.0 Å
shell_rg	38.84 Å
envelope_rg	36.00 Å
shape_rg	35.68 Å
total_rg	35.96 Å
total_atoms	6434
n_residues	773
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	123.3 Å
rg_real	36.43 Å
rg_real_error	1.31 Å
i0_real	2.2480e+08
i0_real_error	4.2040e+06
rg_reciprocal	36.16 Å
i0_reciprocal	224800000.0000
total_estimate	0.7806
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.8 Å
skewness	0.576
kurtosis	-0.427
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	19030000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.606; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.617; Smooth: 0.709

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Alpha-1,2-mannosyltransferase ALG9
formula_weight	70347.5 kDa
ec_number	2.4.1.259,2.4.1.261
mutation	D82A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6456

GPGGSTMASRGARQRLKGSGASSGDTAPAADKLRELLGSREAGGAEHRTELSGNKAGQVWAPEGSTAFKCLLSARLCAALLSNISDCAETFNYWEPTHYLIYGEGFQTWEYSPAYAIRSYAYLLLHAWPAAFHARILQTNKILVFYFLRCLLAFVSCICELYFYKAVCKKFGLHVSRMMLAFLVLSTGMFCSSSAFLPSSFCMYTTLIAMTGWYMDKTSIAVLGVAAGAILGWPFSAALGLPIAFDLLVMKHRWKSFFHWSLMALILFLVPVVVIDSYYYGKLVIAPLNIVLYNVFTPHGPDLYGTEPWYFYLINGFLNFNVAFALALLVLPLTSLMEYLLQRFHVQNLGHPYWLTLAPMYIWFIIFFIQPHKEERFLFPVYPLICLCGAVALSALQKCYHFVFQRYRLEHYTVTSNWLALGTVFLFGLLSFSRSVALFRGYHGPLDLYPEFYRIATDPTIHTVPEGRPVNVCVGKEWYRFPSSFLLPDNWQLQFIPSEFRGQLPKPFAEGPLATRIVPTDMNDQNLEEPSRYIDISKCHYLVDLDTMRETPREPKYSSNKEEWISLAYRPFLDASRSSKLLRAFYVPFLSDQYTVYVNYTILKPRKAKQIRKKSGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Hs9-8 Fab heavy chain
formula_weight	25638.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EISEVQLVESGGGLVQPGGSLRLSCAASGFNIYYSSIHWVRQAPGKGLEWVASISSSSGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYWDGWQYSDSWYYSPYAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Source

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

Entity 3 polymer

description	Hs9-8 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 4 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-1-O-phosphono-alpha-D-glucopyranose ;
formula_weight	1315.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	[(3S,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] dihydrogen phosphate
formula_weight	440.6 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	CHOLESTEROL HEMISUCCINATE
formula_weight	486.7 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

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

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	22

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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	2.89 Å
resolution_method	—
num_particles	395345

fit	/app/data/saxs_computation/s6/9s6s/9s6s.fit
pddf	/app/data/pr_computation/s6/9s6s/9s6s.pr.out
profile	/app/data/saxs_computation/s6/9s6s/9s6s.dat

Ternary cryo-EM structure of human ALG9 with Dol25-PP-GlcNAc2Man6, 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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)