9N8N | pdb_00009n8n

Tandem antigen chimera of Pfs230 and Pfs48/45 bound by potent mAbs

PDB DOI: https://doi.org/10.2210/pdb9N8N/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Plasmodium falciparum 3D7
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-02-09 Released: 2026-02-04
Deposition Author(s): Ivanochko, D., Semesi, A., Julien, J.P.
Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.210 (Depositor), 0.211 (DCC)
R-Value Work:
0.174 (Depositor), 0.176 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Tandem antigen chimera of Pfs230 and Pfs48/45 bound by potent mAbs

Ivanochko, D., Semesi, A., Julien, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 135.13 kDa
Atom Count: 9,630
Modeled Residue Count: 1,170
Deposited Residue Count: 1,210
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUPA-39 heavy chain	A	227	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RUPA-39 Kappa chain	B	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RUPA-44 Kappa chain	C [auth E]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RUPA-44 heavy chain	D [auth F]	230	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D [auth F]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Gametocyte surface protein P230,Gametocyte surface protein P45/48	E [auth I]	324	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PFS230, PF230, S230, PF3D7_0209000, PF45/48, PFS45-48, PFS45/48, PF13_0247, PF3D7_1346700
UniProt
Find proteins for P68874 (Plasmodium falciparum (isolate 3D7)) Explore P68874 Go to UniProtKB: P68874
Find proteins for Q8I6T1 (Plasmodium falciparum (isolate 3D7)) Explore Q8I6T1 Go to UniProtKB: Q8I6T1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P68874Q8I6T1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth C]	3		N-Glycosylation	Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain JA [auth F] SDF format, chain LA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain LA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain LA [auth F]	JA [auth F], LA [auth F]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain JA [auth F] Focus chain LA [auth F] Interactions & Density Focus chain JA [auth F] Focus chain LA [auth F]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	N [auth B], P [auth B], T [auth B], U [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain P [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain N [auth B] Focus chain P [auth B] Focus chain T [auth B] Focus chain U [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain PA [auth I] SDF format, chain Q [auth B] SDF format, chain QA [auth I] SDF format, chain R [auth B] SDF format, chain RA [auth I] SDF format, chain SA [auth I] SDF format, chain Z [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain SA [auth I] MOL2 format, chain Z [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth I] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth I] mmCIF format, chain SA [auth I] mmCIF format, chain Z [auth E]	BA [auth E] CA [auth E] DA [auth E] EA [auth E] G [auth A] BA [auth E], CA [auth E], DA [auth E], EA [auth E], G [auth A], H [auth A], I [auth A], KA [auth F], L [auth B], M [auth B], MA [auth F], NA [auth F], O [auth B], OA [auth F], PA [auth I], Q [auth B], QA [auth I], R [auth B], RA [auth I], SA [auth I], Z [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain R [auth B] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain R [auth B] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain Z [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain IA [auth F] SDF format, chain V [auth B] MOL2 format, chain AA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain V [auth B] mmCIF format, chain AA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain V [auth B]	AA [auth E], FA [auth E], GA [auth E], IA [auth F], V [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain IA [auth F] Focus chain V [auth B] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain IA [auth F] Focus chain V [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain HA [auth E] SDF format, chain W [auth B] MOL2 format, chain HA [auth E] MOL2 format, chain W [auth B] mmCIF format, chain HA [auth E] mmCIF format, chain W [auth B]	HA [auth E], W [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain HA [auth E] Focus chain W [auth B] Interactions & Density Focus chain HA [auth E] Focus chain W [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain K [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain K [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	K [auth A], X [auth B], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain K [auth A] Focus chain X [auth B] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.210 (Depositor), 0.211 (DCC)
R-Value Work: 0.174 (Depositor), 0.176 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 227.99	α = 90
b = 80.49	β = 111.46
c = 137.73	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-04

Deposition Author(s):

Ivanochko, D.

Semesi, A.

Julien, J.P.

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-008866 and OPP1156262
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01AI148557-01A1
Canadian Institutes of Health Research (CIHR)	Canada	428410