2Q8B: Malaria antigen AMA1

Structure of the malaria antigen AMA1 in complex with a growth-inhibitory antibody. Determined by X-ray diffraction at 2.3 Å resolution. Released 9 Oct 2007.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Plasmodium falciparum, Mus musculus
Chains: 3
Atoms: 5,598
Mol. weight: 84.49 kDa
Released: 9 Oct 2007

Explore 2Q8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Q8B contains 28 α-helices and 67 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	111-114	4
α-helix	115-117	3
α-helix	119-122	4
β-strand	133-137	5	1
β-strand	140-144	5	1
β-strand	151-152	2	2
β-strand	155-158	4	3
β-strand	168	1	4
α-helix	169-170	2
α-helix	176-178	3
β-strand	182	1	4
α-helix	183-184	2
β-strand	193-194	2	2
α-helix	195-201	7
α-helix	208-210	3
α-helix	213-221	9
β-strand	224	1	5
α-helix	225	1
α-helix	226-228	3
β-strand	238-241	4	2
β-strand	246-249	4	2
β-strand	250	1	4
β-strand	257	1	3
β-strand	276-279	4	3
α-helix	282-284	3
β-strand	287-290	4	2
α-helix	298-301	4
β-strand	306	1	6
β-strand	307-308	2	7
β-strand	311-315	5	8
β-strand	320-322	3	8
α-helix	323	1
β-strand	327-330	4	7
α-helix	334-344	11
β-strand	399-403	5	7
β-strand	408-412	5	7
β-strand	418-420	3	8
β-strand	425-429	5	7
β-strand	437	1	6

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
α-helix	7-9	3
β-strand	10-12	3	15
β-strand	18-25	8	14
β-strand	27	1	5
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-52	8	15
β-strand	57-60	4	15
α-helix	62-64	3
β-strand	65	1	14
β-strand	68-73	6	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-98	7	15
β-strand	101-102	2	15
β-strand	106-110	5	15
α-helix	113-115	3
β-strand	116	1	16
β-strand	119-123	5	17
β-strand	134-144	11	17
β-strand	145	1	16
β-strand	150-153	4	18
β-strand	163-171	9	17
β-strand	173-183	11	17
β-strand	193-198	6	18
β-strand	203-208	6	18

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-14	5	10
β-strand	19-25	7	9
β-strand	33-38	6	10
β-strand	45-49	5	10
β-strand	53-54	2	10
α-helix	55	1
β-strand	62-67	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	85-90	6	10
α-helix	97	1
β-strand	98	1	10
α-helix	99	1
β-strand	102-107	6	10
β-strand	111	1	11
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	145-150	6	13
β-strand	155	1	13
β-strand	159-163	5	12
α-helix	164-167	4
β-strand	173-182	10	12
α-helix	183-188	6
β-strand	191-197	7	13
β-strand	205-210	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apical membrane antigen 1	A	protein	336	Plasmodium falciparum	P22621 (AlphaFold model)
1F9 light chain	L	protein	214	Mus musculus
1F9 heavy chain	H	protein	210	Mus musculus	P01867 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2Q8B_1 Apical membrane antigen 1 (chains A)
GNYMGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSN
TTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAG
NMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDI
SFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVF
ELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNY
NTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE

Sequence of entity 2 (L), FASTA

>2Q8B_2 1F9 light chain (chains L)
SIVMTQTPKFLPVSAGDRVTIICKASQSVSNDVVWYQQKPGQSPKLLIYYASIRYTGVPD
RFTGSGYGTDFTFTISTVQVEDLAVYFCQQGFSSPRTFGGGTKLEINRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (H), FASTA

>2Q8B_3 1F9 heavy chain (chains H)
EVQLQQSGAELLRPGASVKLSCIVSGFKIKDTSMHWVKQRPEQGLEWIGRIDPANDNSEY
DPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCTLSHFWGQGTTLTVSSAKTTPPSV
YPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSV
TVPSSTWPSQTVTCSVAHPASSTTVDKKLE

Primary citation

Structure of the Malaria Antigen AMA1 in Complex with a Growth-Inhibitory Antibody. Coley, A.M., Gupta, A., Murphy, V.J. et al. PLoS Pathog (2007) 3:e138. DOI 10.1371/journal.ppat.0030138 · PubMed

Other PDB entries of the same protein (UniProt P22621 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2Q8A 2.4 Å, Structure of the malaria antigen AMA1 in complex with a growth-inhibitory antibody
9BJH 2.8 Å, Crystal structure of neutralizing human monoclonal antibody 75C8 in complex with AMA1…
9BJG 2.9 Å, Crystal structure of broadly neutralizing human monoclonal antibody 75B10 in complex…
1YXE Structure and inter-domain interactions of domain II from the blood stage malarial…

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