8UX6 | pdb_00008ux6

Structure of Fab201 with a T. parva sporozoite neutralizing B cell epitope of p67

PDB DOI: https://doi.org/10.2210/pdb8UX6/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Theileria parva strain Muguga
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-08 Released: 2024-10-16
Deposition Author(s): Singer, A.U., Gopalsamy, A., Fellouse, F.A., Miersch, S., Sidhu, S.S.
Funding Organization(s): Bill & Melinda Gates Foundation, Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.251 (Depositor), 0.251 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Molecular characterization of a synthetic neutralizing antibody targeting p67 of Theileria parva.

Miersch, S., Singer, A.U., Chen, C., Fellouse, F., Gopalsamy, A., Costa, L.S.E., Lacasta, A., Chege, H., Chege, N., Nene, V., Sidhu, S.S.

(2025) Protein Sci 34: e70153-e70153

PubMed: 40384600 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70153
Primary Citation Related Structures:
8UX6

PubMed Abstract:
The Theileria parva sporozoite surface antigen p67 is a target of the bovine humoral immune response that generates antibodies capable of providing protection against subsequent infection. As a result, p67 has been the subject of efforts aimed at the development of an anti-sporozoite subunit vaccine. Previous studies have identified neutralizing epitopes in the N- and C-terminal regions of the full-length protein and shown that immunization with a C-terminal fragment of p67 (p67C) alone is capable of eliciting protection. To identify additional neutralizing epitopes in p67C, selections were conducted against it using a phage-displayed synthetic antibody library. An antibody that neutralized the sporozoite in vitro was identified, and the crystal structure of a Fab:peptide complex was elucidated. Mutagenesis studies aimed at validating and further characterizing the Fab:peptide interaction identified critical residues involved in binding and neutralization. This study also validates distinct epitopes for previously reported neutralizing antibodies.

Organizational Affiliation

The School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 103.84 kDa
Atom Count: 7,202
Modeled Residue Count: 884
Deposited Residue Count: 956
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab201 light chain	A [auth C], B [auth A]	216	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab201 heavy chain	C [auth B], D	221	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
p67 protein	E, F	41	Theileria parva strain Muguga	Mutation(s): 0
UniProt
Find proteins for Q27040 (Theileria parva) Explore Q27040 Go to UniProtKB: Q27040
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q27040
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE (Subject of Investigation/LOI) Query on EPE Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain R [auth A] MOL2 format, chain H [auth C] MOL2 format, chain R [auth A] mmCIF format, chain H [auth C] mmCIF format, chain R [auth A]	H [auth C], R [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain R [auth A] Interactions & Density Focus chain H [auth C] Focus chain R [auth A]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain I [auth C] SDF format, chain Q [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain I [auth C] MOL2 format, chain Q [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain I [auth C] mmCIF format, chain Q [auth A]	AA [auth B] CA [auth D] DA [auth D] EA [auth D] FA [auth D] AA [auth B], CA [auth D], DA [auth D], EA [auth D], FA [auth D], I [auth C], Q [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth C] Focus chain Q [auth A] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth C] Focus chain Q [auth A]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain Z [auth B] MOL2 format, chain G [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain G [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B]	G [auth C] JA [auth D] KA [auth D] M [auth C] N [auth C] G [auth C], JA [auth D], KA [auth D], M [auth C], N [auth C], O [auth C], P [auth C], S [auth A], V [auth A], W [auth A], X [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain G [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Z [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain U [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain U [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain U [auth A]	K [auth C], L [auth C], U [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain L [auth C] Focus chain U [auth A] Interactions & Density Focus chain K [auth C] Focus chain L [auth C] Focus chain U [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain J [auth C] SDF format, chain T [auth A] SDF format, chain Y [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth C] MOL2 format, chain T [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth C] mmCIF format, chain T [auth A] mmCIF format, chain Y [auth B]	GA [auth D] HA [auth D] IA [auth D] J [auth C] T [auth A] GA [auth D], HA [auth D], IA [auth D], J [auth C], T [auth A], Y [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth C] Focus chain T [auth A] Focus chain Y [auth B] Interactions & Density Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth C] Focus chain T [auth A] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.251 (Depositor), 0.251 (DCC)
R-Value Work: 0.204 (Depositor), 0.204 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.01	α = 69.26
b = 75.56	β = 77.6
c = 90.591	γ = 76.08

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1078791
Other government	Canada	Canada Foundation for Innovation Physical Infrastructure Grant #33363
Other government	Canada	International Development Research Centre Joint Canada-Israel Health Research Program #108404-001