SAXSdb — 9yc3

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nanobody WNb 334 × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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.

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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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9yc3__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9yc3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9yc3__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	19.42 Å
Rg (electron density)	18.30 Å
Total Rg	19.13 Å
Atom count	1786
Residues	245
Excluded volume	31334 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9yc3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism 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

Source Source

Source organism organism	Plasmodium falciparum
Common name common_name	malaria parasite P. falciparum
NCBI taxonomy ID ncbi_taxonomy_id	5833
Host organism 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9yc3__assembly_1__model_1

9yc3__assembly_1__model_1 | I(q)

9yc3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9yc3__assembly_1__model_1

9yc3__assembly_1__model_1 | I(q)

9yc3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)