7LR3 | pdb_00007lr3

Complex of Fab 2/6.14 with domain 3 of P. berghei HAP2

• PDB DOI: https://doi.org/10.2210/pdb7LR3/pdb

• Classification: SURFACTANT PROTEIN/IMMUNE SYSTEM
• Organism(s): Mus musculus, Plasmodium berghei
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2021-02-15 Released: 2021-12-15 
• Deposition Author(s): Feng, J., Dong, X.C., Lu, C.F., Springer, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.292 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

Literature

Structural basis of malaria transmission blockade by a monoclonal antibody to gamete fusogen HAP2.

Feng, J., Dong, X., DeCosta, A., Su, Y., Angrisano, F., Sala, K.A., Blagborough, A.M., Lu, C., Springer, T.A.

(2021) Elife 10

• PubMed: 34939934 
• DOI: https://doi.org/10.7554/eLife.74707
• Primary Citation Related Structures: 
  7LR3, 7LR4


• PubMed Abstract: 
  

  HAP2 is a transmembrane gamete fusogen found in multiple eukaryotic kingdoms and is structurally homologous to viral class II fusogens. Studies in Plasmodium have suggested that HAP2 is an attractive target for vaccines that block transmission of malaria. HAP2 has three extracellular domains, arranged in the order D2, D1, and D3. Here, we report monoclonal antibodies against the D3 fragment of Plasmodium berghei HAP2 and crystal structures of D3 in complex with Fab fragments of two of these antibodies, one of which blocks fertilization of Plasmodium berghei in vitro and transmission of malaria in mosquitoes. We also show how this Fab binds the complete HAP2 ectodomain with electron microscopy. The two antibodies cross-react with HAP2 among multiple plasmodial species. Our characterization of the Plasmodium D3 structure, HAP2 ectodomain architecture, and mechanism of inhibition provide insights for the development of a vaccine to block malaria transmission.

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Organizational Affiliation: 
• Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States.
School of Life Sciences, Nanjing University, Nanjing, China.
Burnet Institute, Melbourne, Australia.
Department of Pathology, University of Cambridge, Cambridge, United Kingdom.
Boston Children's Hospital, Boston, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 124.45 kDa 
• Atom Count: 10,350 
• Modeled Residue Count: 1,032 
• Deposited Residue Count: 1,128 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D3_2/6.14 Fab light chain	A [auth L], F [auth B]	213	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D3_2/6.14 Fab heavy chain	B [auth H], E [auth A]	228	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hapless 2	C [auth D]	123	Plasmodium berghei	Mutation(s): 3  Gene Names: HAP2, GCS1, PB000710.01.0
UniProt
Find proteins for Q4YCF6 (Plasmodium berghei (strain Anka)) Explore Q4YCF6  Go to UniProtKB:  Q4YCF6

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Hapless 2	D [auth C]	123	Plasmodium berghei	Mutation(s): 3  Gene Names: HAP2, GCS1, PB000710.01.0
UniProt
Find proteins for Q4YCF6 (Plasmodium berghei (strain Anka)) Explore Q4YCF6  Go to UniProtKB:  Q4YCF6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	H [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG	G [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	C [auth D]	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.292 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.25	α = 90
b = 122.58	β = 90
c = 168.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XSCALE	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-15 
Deposition Author(s): Feng, J., Dong, X.C., Lu, C.F., Springer, T.A.

Revision History  

• Version 1.0: 2021-12-15
  Type: Initial release
  
• Version 1.1: 2022-01-05
  Changes: Database references
• Version 1.2: 2022-01-19
  Changes: Structure summary
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary