8A44: Duffy binding protein

Plasmodium vivax Duffy binding protein region II bound the DARC ectodomain and monoclonal antibody DB1. Determined by X-ray diffraction at 2.49 Å resolution. Released 7 Jun 2023.

Method: X-ray diffraction
Resolution: 2.49 Å
Organisms: Plasmodium vivax, Homo sapiens
Chains: 4
Atoms: 6,258
Mol. weight: 88.85 kDa
Released: 7 Jun 2023

Explore 8A44 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8A44 contains 38 α-helices and 52 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: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	218-222	5
β-strand	229	1	1
β-strand	238	1	1
α-helix	240-243	4
α-helix	248-252	5
α-helix	255-256	2
α-helix	265-290	26
β-strand	294-296	3	2
α-helix	297-315	19
α-helix	324-336	13
α-helix	342-361	20
α-helix	363-369	7
α-helix	370-372	3
β-strand	375	1	3
α-helix	379-382	4
α-helix	388-412	25
β-strand	418-419	2	4
β-strand	423-424	2	4
α-helix	425-427	3
α-helix	430-461	32
α-helix	474-481	8
α-helix	487-494	8
α-helix	499-505	7

Chain B: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	22-28	7
α-helix	36-37	2
β-strand	38	1	3
β-strand	44-46	3	2

Chain C: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	5
α-helix	26-28	3
β-strand	29-31	3	6
β-strand	37-44	8	5
α-helix	48-50	3
β-strand	52-58	7	6
β-strand	65-71	7	6
β-strand	77-79	3	6
β-strand	88-92	5	5
α-helix	93-95	3
β-strand	97-102	6	5
α-helix	107-109	3
β-strand	111-120	10	6
β-strand	127-132	6	6
β-strand	136-140	5	6
β-strand	146	1	7
α-helix	147-148	2
β-strand	149-153	5	8
α-helix	157-159	3
β-strand	160-161	2	8
β-strand	164-174	11	8
β-strand	175	1	7
β-strand	180-183	4	9
α-helix	184-186	3
β-strand	188	1	9
β-strand	192-194	3	8
α-helix	195-197	3
β-strand	198-199	2	8
β-strand	205-214	10	8
α-helix	215-217	3
β-strand	224-229	6	9
α-helix	230-232	3
β-strand	234-239	6	9
α-helix	240	1

Chain D: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	10
β-strand	29-32	4	11
β-strand	38-44	7	10
β-strand	52-57	6	11
β-strand	64-68	5	11
β-strand	72-73	2	11
α-helix	74	1
β-strand	81-85	5	10
β-strand	89-94	6	10
α-helix	99-101	3
β-strand	104-109	6	11
β-strand	117-118	2	11
β-strand	122-126	5	11
β-strand	131	1	12
α-helix	132-133	2
β-strand	134-138	5	13
α-helix	139-141	3
α-helix	142-147	6
β-strand	149-159	11	13
β-strand	160	1	12
β-strand	164-170	7	14
β-strand	173-174	2	14
α-helix	175	1
β-strand	179-183	5	13
α-helix	184-187	4
β-strand	193-202	10	13
α-helix	203-207	5
β-strand	211-218	8	14
β-strand	225-230	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Duffy binding protein	A	protein	294	Plasmodium vivax	P22290 (AlphaFold model)
Atypical chemokine receptor 1	B	protein	60	Homo sapiens	Q16570 (AlphaFold model)
Heavy chain of monoclonal antibody DB1	C	protein	225	Homo sapiens
Light chain of monoclonal antibody DB1	D	protein	213	Homo sapiens

Sequence of entity 1 (A), FASTA

>8A44_1 Duffy binding protein (chains A)
KNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDTNFHRDITFRKLYLKR
KLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVVENNLRS
IFGTDEKAQQRRKQWWNESKAQIWTAMMYSVKKRLKGNFIWICKLNVAVNIEPQIYRWIR
EWGRDYVSELPTEVQKLKEKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKNQWDVLS
NKFISVKNAEKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCS

Sequence of entity 2 (B), FASTA

>8A44_2 Atypical chemokine receptor 1 (chains B)
MGNALHRAELSPSTENSSQLDFEDVWNSSYGVNDSFPDGDYDANLEAAAPAHSANLLDDS

Sequence of entity 3 (C), FASTA

>8A44_3 Heavy chain of monoclonal antibody DB1 (chains C)
EVQLVQSGAEVKKPGESLKISCKGSGYSFTDYWIGWVRQMPGKGLEWMGIIYAGDSDTRY
SPSFQGQVTISADKSISTASLQWSSLKASDTAMYYCARLAYDSSGYYYAFDIWGQGTMVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Sequence of entity 4 (D), FASTA

>8A44_4 Light chain of monoclonal antibody DB1 (chains D)
IVMTQSPSSLSASVGDRVTITCRASQTISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSR
FSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLITFGQGTRLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Primary citation

Structural basis for DARC binding in reticulocyte invasion by Plasmodium vivax. Moskovitz, R., Pholcharee, T., DonVito, S.M. et al. Nat Commun (2023) 14:3637-3637. DOI 10.1038/s41467-023-39357-w · 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…
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
6R2S 3.04 Å, The structure of Plasmodium vivax Duffy binding protein (PvDBP) bound to human antibody…
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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