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9s36

Cryo-EM structure of Candida albicans Vrg4 bound to an inhibitory nanobody and GDP-Mannose.

Method: ELECTRON MICROSCOPY D_max: 86.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s36
deposition_date	2025-07-23
last_revision	2025-09-03
title	Cryo-EM structure of Candida albicans Vrg4 bound to an inhibitory nanobody and GDP-Mannose.
keywords	GDP-Mannose transporter; Membrane Protein; Nucleotide Sugar Transporter, TRANSPORT PROTEIN; TRANSPORT 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	25.37 Å
rg_electron	24.62 Å
i0	36415400.00
molecular_weight	49045.0 kDa
excluded_volume	62467 Å³
envelope_volume	76411 Å³
shell_volume	26710 Å³
envelope_diameter	89.1 Å
shell_rg	31.13 Å
envelope_rg	24.83 Å
shape_rg	24.59 Å
total_rg	25.50 Å
total_atoms	6929
n_residues	441
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	86.0 Å
rg_real	25.46 Å
rg_real_error	0.59 Å
i0_real	3.6420e+07
i0_real_error	5.2600e+05
rg_reciprocal	25.43 Å
i0_reciprocal	36410000.0000
total_estimate	0.8677
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.9 Å
skewness	0.478
kurtosis	-0.211
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	7218000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.974

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	GDP-mannose transporter
formula_weight	37183.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6929

MDSKHSTSSSSSGSLATRISNSGPISIAAYCLSSILMTVTNKYVLSGFSFNLNFFLLAVQSIVCIVTIGSLKSLNIITYRQFNKDEAKKWSPIAFLLVAMIYTSSKALQYLSIPVYTIFKNLTIILIAYGEVIWFGGKVTTMALSSFLLMVLSSVIAYYGDNAAVKSHDDAFALYLGYFWMLTNCFASAAFVLIMRKRIKLTNFKDFDTMYYNNLLSIPILLICSFIFEDWSSANVSLNFPADNRVTTITAMILSGASSVGISYCSAWCVRVTSSTTYSMVGALNKLPIALSGLIFFEAAVNFWSVSSIFVGFGAGLVYAVAKQKQQKEQSQQLPTTK

Source

organism	Candida albicans
ncbi_taxonomy_id	5476
host_organism	Saccharomyces cerevisiae

Entity 2 polymer

description	lama nanobody
formula_weight	13781.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QVQLVESGGGLVQAGGSLRLSCAASGRTFRSYTLGWFRQAPGKEREFVAAIKWSTDTTYYADSVKGRFTISGDNAKNTVYLQMNSLKPEDTAVYFCAARSLSTVIAGPEIPWPYNSWGQGTQVTVSS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
formula_weight	605.3 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	3.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.40 Å
resolution_method	—
num_particles	51142

fit	/app/data/saxs_computation/s3/9s36/9s36.fit
pddf	/app/data/pr_computation/s3/9s36/9s36.pr.out
profile	/app/data/saxs_computation/s3/9s36/9s36.dat

Cryo-EM structure of Candida albicans Vrg4 bound to an inhibitory nanobody and GDP-Mannose.

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)