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

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Male gamete fusion factor HAP2

Plasmodium falciparum

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 500–620	Not recorded	Nanobody WNb 334 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.7；293 K；0.1 M HEPES pH 7.7, 27% w/v PEG 3350	Resolution 2.80 Å R-free 0.253

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q8IJQ3_PLAF7
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–123； UniProt 500–620

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

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

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.42 Å
Radius of gyration Rg (electron density) rg_electron	18.30 Å
Forward intensity I(0) i0	12563600.00
Molecular weight molecular_weight	25448.0 kDa
Excluded volume excluded_volume	31334 Å³
Envelope volume envelope_volume	37114 Å³
Hydration-shell volume shell_volume	17216 Å³
Envelope diameter envelope_diameter	63.2 Å
Shell Rg shell_rg	24.14 Å
Envelope Rg envelope_rg	18.51 Å
Shape Rg shape_rg	18.31 Å
Total Rg total_rg	19.13 Å
Total atoms total_atoms	1786
Residues n_residues	245
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	63.6 Å
Rg (real space) rg_real	19.34 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	1.2560e+07
I(0) uncertainty (real space) i0_real_error	1.7370e+05
Rg (reciprocal space) rg_reciprocal	19.35 Å
I(0) (reciprocal space) i0_reciprocal	12560000.0000
Solution quality estimate total_estimate	0.8935
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.185
Kurtosis Kurtosis kurtosis	-0.469
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3075000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Nanobody WNb 334
Molecular weight formula_weight	14617.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1792

QVQLQESGGGLVQPGGSLRLSCAASGFTLDDYAIGWFRQDPGKGREGVSCISLSDGSTYYADAVTGRFTISRDNAKDTVYLQMNSLKPEDTAVYYCAALSQKQMTTVQAMCAVPIANYWGQGTQVTVSSHHHHHH

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Male gamete fusion factor HAP2
Molecular weight formula_weight	15911.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ADPVSYGTITHITIPKDCSSNQTNSKECILVVHTWNNNKTIGANFSCHVLCVDKSTQQVATHISPISKINAHIDANKNYAFYFIIKFLINKKITSNCTAILKDADGRECSKLSFNLTSKETINSGRENLYFQGHHHHHHHH

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI Class编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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8. Citations (1)

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Unit-cell length a length_a	76.474 Å
Unit-cell length b length_b	76.474 Å
Unit-cell length c length_c	95.712 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	38.790 Å
R factor r_factor	0.2253
R_work r_work	0.2238
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Male gamete fusion factor HAP2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)