6MB3 | pdb_00006mb3

Cryo-EM structure of the circumsporozoite protein of Plasmodium falciparum with a vaccine-elicited antibody reveals maturation of inter-antibody contacts

External Resource: Annotation

Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
S	V-set_3	e6mb3S1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
Q [auth R]	V-set_3	e6mb3R1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
O [auth Q]	V-set_3	e6mb3Q1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
M [auth P]	V-set_3	e6mb3P1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
K [auth O]	V-set_3	e6mb3O1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
I [auth N]	V-set_3	e6mb3N1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
G [auth M]	V-set_3	e6mb3M1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
E [auth K]	V-set_3	e6mb3K1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
C [auth L]	V-set_3	e6mb3L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
R [auth J]	V-set_12	e6mb3J1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
P [auth I]	V-set_12	e6mb3I1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
N [auth G]	V-set_12	e6mb3G1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
L [auth F]	V-set_12	e6mb3F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
J [auth D]	V-set_12	e6mb3D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
H [auth C]	V-set_12	e6mb3C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
F [auth B]	V-set_12	e6mb3B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
D [auth A]	V-set_12	e6mb3A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
B [auth H]	V-set_12	e6mb3H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C [auth L], E [auth K], G [auth M], I [auth N], K [auth O], C [auth L], E [auth K], G [auth M], I [auth N], K [auth O], M [auth P], O [auth Q], Q [auth R], S	Fab 311	L-LAMBDA	Homo sapiens (human)	IGLV1-4001, IGLJ302, IGLC701, IGLC702	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202548-0)
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	Fab 311	VH-CH1	Homo sapiens (human)	IGHV3-3301, IGHV3-3304, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG111	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202548-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L], E [auth K], G [auth M], I [auth N], K [auth O], C [auth L], E [auth K], G [auth M], I [auth N], K [auth O], M [auth P], O [auth Q], Q [auth R], S	Light Chain	IGLV1	Lambda	plasmodium falciparum recombinant shortened csp	SAbDab (2025-12-12)
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	Heavy Chain	IGHV3	-	plasmodium falciparum recombinant shortened csp	SAbDab (2025-12-12)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth L], E [auth K], G [auth M], I [auth N], K [auth O], C [auth L], E [auth K], G [auth M], I [auth N], K [auth O], M [auth P], O [auth Q], Q [auth R], S	Fab311 light chain	-	-	-
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	Fab311 heavy chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
A [auth E]	Plasmodium falciparum recombinant shortened CSP	host cell surface binding binding protein binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding	biological process involved in interspecies interaction between organisms symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell viral process viral life cycle entry into host cell by a symbiont-containing vacuole	cell surface cellular anatomical structure membrane side of membrane cell periphery plasma membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	IPR003597	Immunoglobulin C1-set	Domain
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	IPR007110	Immunoglobulin-like domain	Domain
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	IPR050380	Immune Recognition and Response Modulators	Family
B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], B [auth H], D [auth A], F [auth B], H [auth C], J [auth D], L [auth F], N [auth G], P [auth I], R [auth J]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth E]	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
A [auth E]	IPR003067	Plasmodium circumsporozoite protein	Family
A [auth E]	IPR051860	Plasmodium Circumsporozoite Invasion Protein	Family
A [auth E]	IPR036383	Thrombospondin type-1 repeat superfamily	Homologous Superfamily

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.