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9s35

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

Method: ELECTRON MICROSCOPY D_max: 89.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s35
deposition_date	2025-07-23
last_revision	2025-09-03
title	Cryo-EM structure of Candida albicans Vrg4 bound to an inhibitory nanobody.
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	24.72 Å
rg_electron	24.09 Å
i0	33245800.00
molecular_weight	47096.0 kDa
excluded_volume	60124 Å³
envelope_volume	72696 Å³
shell_volume	26022 Å³
envelope_diameter	92.0 Å
shell_rg	30.47 Å
envelope_rg	24.30 Å
shape_rg	24.08 Å
total_rg	24.93 Å
total_atoms	3315
n_residues	428
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	89.0 Å
rg_real	24.84 Å
rg_real_error	0.84 Å
i0_real	3.3250e+07
i0_real_error	4.7460e+05
rg_reciprocal	24.82 Å
i0_reciprocal	33250000.0000
total_estimate	0.7513
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	25.4 Å
skewness	0.504
kurtosis	-0.126
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	7340000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.656; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.801; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Llama Nanobody
formula_weight	13376.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	3361

QVQLVESGGGLVQPGGSLRLSCAASGSISEINVMGWYRQAPGKQRELVARITTGGSTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYMCNAHRRVVMEWGPLGYDYWGQGTQVTVSS

Source

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

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	A

MDSKHSTSSSSSGSLATRISNSGPISIAAYCLSSILMTVTNKYVLSGFSFNLNFFLLAVQSIVCIVTIGSLKSLNIITYRQFNKDEAKKWSPIAFLLVAMIYTSSKALQYLSIPVYTIFKNLTIILIAYGEVIWFGGKVTTMALSSFLLMVLSSVIAYYGDNAAVKSHDDAFALYLGYFWMLTNCFASAAFVLIMRKRIKLTNFKDFDTMYYNNLLSIPILLICSFIFEDWSSANVSLNFPADNRVTTITAMILSGASSVGISYCSAWCVRVTSSTTYSMVGALNKLPIALSGLIFFEAAVNFWSVSSIFVGFGAGLVYAVAKQKQQKEQSQQLPTTK

Source

organism	Candida albicans
ncbi_taxonomy_id	5476
host_organism	Saccharomyces cerevisiae

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	7

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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	3.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.00 Å
resolution_method	—
num_particles	348612

fit	/app/data/saxs_computation/s3/9s35/9s35.fit
pddf	/app/data/pr_computation/s3/9s35/9s35.pr.out
profile	/app/data/saxs_computation/s3/9s35/9s35.dat

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

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 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)