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9wno

Cryo-EM structure of Candida glabrata GPI mannosyltransferase I bound to Dol-P-Man

Method: ELECTRON MICROSCOPY D_max: 129.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wno
deposition_date	2025-09-05
title	Cryo-EM structure of Candida glabrata GPI mannosyltransferase I bound to Dol-P-Man
keywords	GT-C, GPI, Mannosyltransferase, MEMBRANE PROTEIN; MEMBRANE 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	35.18 Å
rg_electron	35.20 Å
i0	123258000.00
molecular_weight	96361.0 kDa
excluded_volume	123540 Å³
envelope_volume	157150 Å³
shell_volume	39542 Å³
envelope_diameter	132.5 Å
shell_rg	38.83 Å
envelope_rg	35.29 Å
shape_rg	35.14 Å
total_rg	35.69 Å
total_atoms	6818
n_residues	814
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	129.6 Å
rg_real	35.55 Å
rg_real_error	1.40 Å
i0_real	1.2330e+08
i0_real_error	2.1190e+06
rg_reciprocal	35.32 Å
i0_reciprocal	123200000.0000
total_estimate	0.7913
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	34.6 Å
skewness	0.643
kurtosis	-0.071
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	25420000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.561; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.700; Smooth: 0.898

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	GPI mannosyltransferase 1
formula_weight	50289.3 kDa
ec_number	2.4.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6818

MFKLGTIGLLSLAVLLRIAFFLFGVYQDEHFTVKYTDIDYQVFNDAAWFVAHRKSPYNRDTYRYTPLLSWLLLPNHMIPWFHFGKLIFVLCDLATGVLILQMLKKLKSKYRYGTDRMTIMAAIWLLNPMVITISTRGNAESVLCFLILSFLYCFLCEQYLLGGLLFGLSIHFKIYPIIYALPIAIYVAAAHYNKTQSVFKSSFKLFLVGFSTLIVLILLTVFMYMLYGDKFIDQTYLYHIYRTDHRHNFSVWNMLLYFNSALPKTSELSKFVFLPQMIIVLAISLTQLRRPSSFPLLCNVLFLETFAFVTFNKVCTSQYFIWYLIFLPFVLYNTRISMRRGIVMLVVWVATQALWLRQGYLLEFEGQNVFYPGLFCASVGFFVSNAWILGQFIEDTIIQNDYVYRIEPSESRSKDSAVIDKPAIAKTEKAE

Source

organism	Nakaseomyces glabratus
ncbi_taxonomy_id	5478
host_organism	Saccharomyces cerevisiae

Entity 2 polymer

description	Protein PBN1
formula_weight	47799.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MESVRHRIALLFANEADIQDVETVEDGVIVFPNSNITIQDRWTYAIDYELDSIRRISWRNPSSTRQFSVIESRLAPGFNIYSNDKEARLNLFGIQPVYSPMYKSLHSETWKSINEILPGGKNLNIPWNPELCDYDILITANTVQVFSYCSLVEKKKFVKDAGKVEIGLFHVDTEDEEDINLSGLRCTWEDTSNNIGKCEKTTLFYKPFHLYVDDSSDIAPITIENTNGLHPKMKIDLSGIRKDKDCRHFVFSQLPSEIFVDKFQSPGSIVFGLDDLELPDYKVNSLSWGSESIVTLKEGQINEITYFSRYLEPKERASNKTVGFEPILFKACQVGKEEDLSNPFYSRSLGYEAYFSENTKFYHINSTSVHVNIPYPNKNDIGNIEYTTFGIVVLAICYLIYKLLRPSRKLSTVKRD

Source

organism	Nakaseomyces glabratus
ncbi_taxonomy_id	5478
host_organism	Saccharomyces cerevisiae

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	dolichyl phosphate mannose
formula_weight	1011.4 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	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	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	3.480 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.48 Å
resolution_method	—
num_particles	80856

fit	/app/data/saxs_computation/wn/9wno/9wno.fit
pddf	/app/data/pr_computation/wn/9wno/9wno.pr.out
profile	/app/data/saxs_computation/wn/9wno/9wno.dat

Cryo-EM structure of Candida glabrata GPI mannosyltransferase I bound to Dol-P-Man

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)