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9yc3

Crystal structure of malaria transmission-blocking antigen PfHAP2 domain 3 in complex with nanobody WNb 334

Method: X-RAY DIFFRACTION D_max: 63.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yc3
deposition_date	2025-09-18
title	Crystal structure of malaria transmission-blocking antigen PfHAP2 domain 3 in complex with nanobody WNb 334
keywords	Transmission-blocking, Nanobody, Fusogen, Malaria, PROTEIN BINDING; PROTEIN BINDING
method	X-RAY DIFFRACTION

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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	19.42 Å
rg_electron	18.30 Å
i0	12563600.00
molecular_weight	25448.0 kDa
excluded_volume	31334 Å³
envelope_volume	37114 Å³
shell_volume	17216 Å³
envelope_diameter	63.2 Å
shell_rg	24.14 Å
envelope_rg	18.51 Å
shape_rg	18.31 Å
total_rg	19.13 Å
total_atoms	1786
n_residues	245
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	63.6 Å
rg_real	19.34 Å
rg_real_error	0.38 Å
i0_real	1.2560e+07
i0_real_error	1.7370e+05
rg_reciprocal	19.35 Å
i0_reciprocal	12560000.0000
total_estimate	0.8935
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.3 Å
skewness	0.185
kurtosis	-0.469
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	3075000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Nanobody WNb 334
formula_weight	14617.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1792

QVQLQESGGGLVQPGGSLRLSCAASGFTLDDYAIGWFRQDPGKGREGVSCISLSDGSTYYADAVTGRFTISRDNAKDTVYLQMNSLKPEDTAVYYCAALSQKQMTTVQAMCAVPIANYWGQGTQVTVSSHHHHHH

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Escherichia coli

Entity 2 polymer

description	Male gamete fusion factor HAP2
formula_weight	15911.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

ADPVSYGTITHITIPKDCSSNQTNSKECILVVHTWNNNKTIGANFSCHVLCVDKSTQQVATHISPISKINAHIDANKNYAFYFIIKFLINKKITSNCTAILKDADGRECSKLSFNLTSKETINSGRENLYFQGHHHHHHHH

Source

organism	Plasmodium falciparum
common_name	malaria parasite P. falciparum
ncbi_taxonomy_id	5833
host_organism	Spodoptera frugiperda

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6

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6. Citations (1)

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length_a	76.474 Å
length_b	76.474 Å
length_c	95.712 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.800 Å
resolution_low	38.790 Å
r_factor	0.2253
r_work	0.2238
r_free	0.2534

fit	/app/data/saxs_computation/yc/9yc3/9yc3.fit
pddf	/app/data/pr_computation/yc/9yc3/9yc3.pr.out
profile	/app/data/saxs_computation/yc/9yc3/9yc3.dat

Crystal structure of malaria transmission-blocking antigen PfHAP2 domain 3 in complex with nanobody WNb 334

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

Diffraction

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)