6R2S: Plasmodium vivax Duffy binding protein

The structure of Plasmodium vivax Duffy binding protein (PvDBP) bound to human antibody DB9. Determined by X-ray diffraction at 3.04 Å resolution. Released 27 Mar 2019.

Method: X-ray diffraction
Resolution: 3.04 Å
Organisms: Homo sapiens, Plasmodium vivax (strain Salvador I)
Chains: 3
Atoms: 5,752
Mol. weight: 90.56 kDa
Released: 27 Mar 2019

Explore 6R2S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R2S contains 29 α-helices and 48 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: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	1
β-strand	29-33	5	2
β-strand	38-48	11	1
β-strand	52-57	6	2
β-strand	64-68	5	2
β-strand	72-73	2	2
β-strand	81-94	14	1
α-helix	99-101	3
β-strand	103-109	7	2
α-helix	115	1
β-strand	116-117	2	2
β-strand	121-126	6	2
β-strand	130	1	3
α-helix	131-132	2
β-strand	133-137	5	4
α-helix	138-140	3
α-helix	141-144	4
β-strand	148-158	11	4
β-strand	159	1	3
β-strand	163-169	7	5
β-strand	172-173	2	5
α-helix	174	1
β-strand	178-182	5	4
β-strand	192-201	10	4
α-helix	202-206	5
β-strand	210-217	8	5
β-strand	224-229	6	5

Chain B: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	6
β-strand	30-31	2	7
β-strand	37-44	8	6
β-strand	54-60	7	2
β-strand	67-72	6	2
β-strand	78-80	3	2
β-strand	88-93	6	6
β-strand	98-103	6	6
α-helix	108-110	3
β-strand	112-120	9	2
β-strand	123-127	5	2
β-strand	131-133	3	2
β-strand	134-135	2	7
α-helix	139-140	2
β-strand	141	1	8
β-strand	144-148	5	9
β-strand	159-169	11	9
β-strand	170	1	8
β-strand	175-178	4	10
α-helix	179-181	3
β-strand	187-189	3	9
α-helix	190-192	3
β-strand	193-194	2	9
β-strand	200-209	10	9
α-helix	210-212	3
β-strand	213	1	11
β-strand	216	1	11
β-strand	219-224	6	10
β-strand	229-234	6	10

Chain C: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	218-222	5
β-strand	229	1	12
β-strand	238	1	12
α-helix	240-243	4
α-helix	248-252	5
α-helix	259-262	4
α-helix	265-290	26
α-helix	297-315	19
α-helix	324-336	13
α-helix	342-351	10
α-helix	354-361	8
α-helix	363-368	6
α-helix	379-382	4
α-helix	388-415	28
β-strand	418-419	2	13
β-strand	423-424	2	13
α-helix	425-428	4
α-helix	430-463	34
α-helix	474-481	8
α-helix	487-494	8
α-helix	499-505	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody DB9 light chain	A	protein	233	Homo sapiens
Antibody DB9 heavy chain	B	protein	278	Homo sapiens
Duffy receptor	C	protein	300	Plasmodium vivax (strain Salvador I)	P22290 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6R2S_1 Antibody DB9 light chain (chains A)
MGWSCIILFLVATATGVHGDIVMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQRPG
KAPRLLIYKASSLLSGVPSRFGGSGSGTDFTLTISSLQPDDFATYHCQHYNTYPWTFGQG
TKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQE
SVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>6R2S_2 Antibody DB9 heavy chain (chains B)
HPLCLSLHRCPLPGPTAPRFYRLNSTMGWSCIILFLVATATGVHSEVQLQESGPGLVKPS
ETLSLTCTVSGGSVSSSTYYWGWVRQPPGKGLEWIGSIYYSGSTYYNPSLKSRVTISVDT
SKNQFSLKLSSVTAADTAVYYCARDGTGALDLWGRGTLVTVSSASTKGPSVFPLAPSSKS
TSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLG
TQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPDPST

Sequence of entity 3 (C), FASTA

>6R2S_3 Duffy receptor (chains C)
SGNTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDTNFHRDITFR
KLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVV
ENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAMMYSVKKRLKGNFIWICKLNVAVNIEPQ
IYRWIREWGRDYVSELPTEVQKLKEKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKN
QWDVLSNKFISVKNAEKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCS

Primary citation

Structural basis for inhibition of Plasmodium vivax invasion by a broadly neutralizing vaccine-induced human antibody. Rawlinson, T.A., Barber, N.M., Mohring, F. et al. Nat Microbiol (2019) 4:1497-1507. DOI 10.1038/s41564-019-0462-1 · PubMed

Other PDB entries of the same protein (UniProt P22290 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EZE 1.55 Å, Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to…
3RRC 1.95 Å, Crystal Structure of Region II from Plasmodium vivax Duffy Binding Protein
4NUU 1.95 Å, Heterotrimer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP)…
4YFS 2.1 Å, Structure of the synthetic Duffy Binding Protein (DBP) antigen DEKnull relevant for…
8A44 2.49 Å, Plasmodium vivax Duffy binding protein region II bound the DARC ectodomain and…
4NUV 2.6 Å, Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein…
6OAN 2.9 Å, Structure of DBP in complex with human neutralizing antibody 053054
6OAO 3.5 Å, Structure of DBP in complex with human neutralizing antibody 092096
5F3J 4.0 Å, Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10

Browse structure collections

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