7UFO | pdb_00007ufo

Structure of PfCSP peptide 21 with antibody P3-42

• PDB DOI: https://doi.org/10.2210/pdb7UFO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Plasmodium falciparum
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-03-23 Released: 2023-04-12 
• Deposition Author(s): Tripathi, P., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structure of PfCSP peptide 21 with antibody P3-42

Tripathi, P., Kwong, P.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.41 kDa 
• Atom Count: 3,774 
• Modeled Residue Count: 452 
• Deposited Residue Count: 461 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P3-42 Fab Heavy chain	A [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P3-42 Fab Light chain	B [auth L]	220	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PfCSP peptide 21	C [auth A]	15	Plasmodium falciparum	Mutation(s): 0
UniProt
Find proteins for Q7K740 (Plasmodium falciparum (isolate 3D7)) Explore Q7K740  Go to UniProtKB:  Q7K740

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth H], F [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth H], G [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.505	α = 90
b = 60.691	β = 106.18
c = 86.502	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Tripathi, P., Kwong, P.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary