9YGI | pdb_00009ygi

Cryo-EM structure of L9-21 in complex with Plasmodium falciparum circumsporozoite protein (PfCSP)

PDB DOI: https://doi.org/10.2210/pdb9YGI/pdb
EM Map EMD-72925: EMDB EMDataResource

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

Deposited: 2025-09-29 Released: 2026-07-29
Deposition Author(s): Tripathi, P., Morano, N.C., Shapiro, L., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9YGI

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

Literature

Cryo-EM structure of L9-21 in complex with Plasmodium falciparum circumsporozoite protein (PfCSP)

Tripathi, P., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 118.42 kDa
Atom Count: 5,524
Modeled Residue Count: 704
Deposited Residue Count: 1,075
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L9-21 heavy chain	A [auth H], C [auth M], E [auth O]	119	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L9-21 light chain	B [auth L], D [auth N], F [auth P]	107	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Circumsporozoite protein	G	397	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: CSP, PF3D7_0304600
UniProt
Find proteins for Q7K740 (Plasmodium falciparum (isolate 3D7)) Explore Q7K740 Go to UniProtKB: Q7K740
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7K740
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20_4459
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-29

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-07-29
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.