6AZM: 580 germline antibody

Crystal structure of the 580 germline antibody bound to circumsporozoite protein NANP 5-mer. Determined by X-ray diffraction at 1.6 Å resolution. Released 13 Dec 2017.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Homo sapiens, Plasmodium falciparum
Chains: 6
Atoms: 7,851
Mol. weight: 99.39 kDa
Released: 13 Dec 2017

Explore 6AZM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AZM contains 37 α-helices and 94 β-strands across 4 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	27C-27D	2	3
β-strand	30-31	2	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
α-helix	155	1
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-187	5
β-strand	191-197	7	6
β-strand	205-210	6	6

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	46-51	6	9
β-strand	57-59	3	9
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-94	7	9
β-strand	103	1	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	115-116	2
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
α-helix	128-130	3
β-strand	131-132	2	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	159	1	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-185	10	11
α-helix	186-188	3
β-strand	195-200	6	12
α-helix	201-203	3
β-strand	205-210	6	12

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	27C-27D	2	15
β-strand	30-31	2	15
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-90	7	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-107	6	14
β-strand	111	1	16
α-helix	112-113	2
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	145-150	6	18
β-strand	153-154	2	18
α-helix	155	1
β-strand	159-163	5	17
α-helix	164-167	4
β-strand	173-182	10	17
α-helix	183-187	5
β-strand	191-197	7	18
β-strand	205-210	6	18

Chain D: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	21
β-strand	46-51	6	21
β-strand	57-59	3	21
α-helix	61-63	3
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-94	7	21
β-strand	103	1	21
β-strand	107-109	3	21
β-strand	110-111	2	20
α-helix	114-116	3
β-strand	117	1	22
α-helix	118-119	2
β-strand	120-124	5	23
α-helix	128-130	3
β-strand	131-132	2	23
β-strand	135-145	11	23
β-strand	146	1	22
β-strand	151-154	4	24
α-helix	155-157	3
β-strand	159	1	24
β-strand	163-165	3	23
α-helix	166-168	3
β-strand	169-170	2	23
β-strand	176-185	10	23
α-helix	186-188	3
β-strand	195-200	6	24
α-helix	201-203	3
β-strand	205-210	6	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
580 germline antibody, light chain	A, C	protein	219	Homo sapiens
580 germline antibody, heavy chain	B, D	protein	225	Homo sapiens
Circumsporozoite protein NANP 5-mer	E, F	protein	20	Plasmodium falciparum	P02893 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6AZM_1 580 germline antibody, light chain (chains A, C)
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPITFGQGTRLEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 2 (B, D), FASTA

>6AZM_2 580 germline antibody, heavy chain (chains B, D)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDPGGDSSPAGRTWFDPWGQGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 3 (E, F), FASTA

>6AZM_3 Circumsporozoite protein NANP 5-mer (chains E, F)
NANPNANPNANPNANPNANP

Primary citation

Natural Parasite Exposure Induces Protective Human Anti-Malarial Antibodies. Triller, G., Scally, S.W., Costa, G. et al. Immunity (2017) 47:1197-1209.e10. DOI 10.1016/j.immuni.2017.11.007 · PubMed

Other PDB entries of the same protein (UniProt P02893 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WFY 1.23 Å, Crystal structure of Fab224 in complex with NPNA4 peptide from circumsporozoite protein
6WG0 1.6 Å, Crystal structure of Fab366 in complex with NPNA3 peptide from circumsporozoite protein
6UC5 1.75 Å, Fab397 in complex with NPNA peptide
7RD4 1.75 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…
6B5R 1.77 Å, Structure of PfCSP peptide 21 with human antibody CIS42
6B5M 1.79 Å, Structure of PfCSP peptide 21 with human protective antibody CIS43
7RD3 1.81 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…
6WFZ 1.84 Å, Crystal structure of Fab399 in complex with NPNA3 peptide from circumsporozoite protein
6D0X 1.85 Å, Crystal structure of chimeric H.2140 / K.1210 Fab in complex with circumsporozoite…
6UUD 1.85 Å, Crystal structure of antibody 5D5 in complex with PfCSP N-terminal peptide
6W00 1.85 Å, Crystal structure of Fab239 in complex with NPNA2 peptide from circumsporozoite protein
7RD9 1.91 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…

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