1Z1Y | pdb_00001z1y

Crystal structure of Methylated Pvs25, an ookinete protein from Plasmodium vivax

• PDB DOI: https://doi.org/10.2210/pdb1Z1Y/pdb

• Classification: CELL ADHESION
• Organism(s): Plasmodium vivax
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2005-03-07 Released: 2005-12-06 
• Deposition Author(s): Saxena, A.K., Singh, K., Su, H.P., Klein, M.M., Stowers, A.W., Saul, A.J., Long, C.A., Garboczi, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.276 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

The essential mosquito-stage P25 and P28 proteins from Plasmodium form tile-like triangular prisms

Saxena, A.K., Singh, K., Su, H.P., Klein, M.M., Stowers, A.W., Saul, A.J., Long, C.A., Garboczi, D.N.

(2006) Nat Struct Mol Biol 13: 90-91

• PubMed: 16327807 
• DOI: https://doi.org/10.1038/nsmb1024
• Primary Citation of Related Structures:  
  1Z1Y, 1Z27, 1Z3G


• PubMed Abstract: 
  

  P25 and P28 proteins are essential for Plasmodium parasites to infect mosquitoes and are leading candidates for a transmission-blocking malaria vaccine. The Plasmodium vivax P25 is a triangular prism that could tile the parasite surface. The residues forming the triangle are conserved in P25 and P28 from all Plasmodium species. A cocrystal structure shows that a transmission-blocking antibody uses only its heavy chain to bind Pvs25 at a vertex of the triangle.

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Organizational Affiliation: 
• Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases (NIAID), US National Institutes of Health (NIH), Twinbrook 2, 12441 Parklawn Drive, Rockville, Maryland 20852, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.63 kDa 
• Atom Count: 2,829 
• Modeled Residue Count: 352 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ookinete surface protein Pvs25	A, B	186	Plasmodium vivax	Mutation(s): 18
UniProt
Find proteins for O96555 (Plasmodium vivax) Explore O96555  Go to UniProtKB:  O96555

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YB	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.276 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.164	α = 90
b = 43.7	β = 103.15
c = 65.65	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-06 
Deposition Author(s): Saxena, A.K., Singh, K., Su, H.P., Klein, M.M., Stowers, A.W., Saul, A.J., Long, C.A., Garboczi, D.N.

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-20
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary