5MZA: The DBLb domain of PF11_0521 PfEMP1

The DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1. Determined by X-ray diffraction at 2.78 Å resolution. Released 22 Mar 2017.

Method: X-ray diffraction
Resolution: 2.78 Å
Organisms: Plasmodium falciparum 3D7, Homo sapiens
Chains: 2
Atoms: 5,086
Mol. weight: 77.8 kDa
Ligands: 3PO, NAG, IHP
Released: 22 Mar 2017

Explore 5MZA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MZA contains 30 α-helices and 30 β-strands across 2 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: 26 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	741-759	19
α-helix	762-765	4
α-helix	769-771	3
α-helix	782-785	4
α-helix	787-789	3
α-helix	819-821	3
β-strand	822-823	2	1
β-strand	834-835	2	1
α-helix	837-840	4
α-helix	845-848	4
β-strand	852	1	2
β-strand	855	1	2
α-helix	857-860	4
α-helix	862	1
α-helix	866-888	23
α-helix	895-914	20
α-helix	923-941	19
α-helix	945-948	4
α-helix	957-974	18
α-helix	982-984	3
β-strand	987	1	3
β-strand	990	1	3
α-helix	993-995	3
α-helix	998-1019	22
α-helix	1020-1023	4
α-helix	1042-1082	41
α-helix	1094-1096	3
α-helix	1097-1109	13
α-helix	1158-1160	3
α-helix	1162-1169	8
β-strand	1180	1	4
β-strand	1199	1	4
α-helix	1206-1208	3
α-helix	1209-1212	4

Chain B: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	5
β-strand	8-12	5	6
β-strand	15-23	9	5
β-strand	30-34	5	7
β-strand	39-42	4	5
β-strand	49-57	9	5
β-strand	61	1	6
β-strand	64-69	6	7
β-strand	72-77	6	7
β-strand	79-83	5	6
β-strand	84	1	8
β-strand	88-91	4	9
α-helix	92-93	2
β-strand	97-99	3	10
β-strand	103-111	9	9
β-strand	114	1	8
α-helix	116-118	3
β-strand	119-125	7	11
β-strand	128-134	7	11
β-strand	140-147	8	9
α-helix	150-152	3
β-strand	156-164	9	11
α-helix	166-168	3
β-strand	172-176	5	11
β-strand	180-181	2	11
β-strand	183-185	3	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Erythrocyte membrane protein 1 (PfEMP1)	A	protein	488	Plasmodium falciparum 3D7	Q8IHM0
Intercellular adhesion molecule 1	B	protein	186	Homo sapiens	P05362 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MZA_1 Erythrocyte membrane protein 1 (PfEMP1) (chains A)
SNPCAKPHGKKLATVKQIAQYYKRKAYIQLNERGSRSALKGDASQGQYDRGGKADDFKTK
LCEINEKHSNARSNSLNPCNGKDNNKVRFNVGTPWQSGEKIATATDVYLPPRRQHFCTSN
LEYLINGGHQAILNVKNGKINHSFLGDVLLAAKYQAQHTMKDYKSKNDKEGICRAIRYSF
ADIGDIIKGTDLWDKDGGEIKTQNHLVTIFDKIKAQLPKDIKGKYTGTKHLELRKDWWEA
NRDQVWKAMQCGNDNPCSGESDHTPLHDYIPQRLRWMTEWAEWYCKEQSRLYDKLKVCEE
CMRKGESCTKGSGECATCKEACEEYNKEIKKWEQQWDAISYKYLMLYAKARITAINGGPG
YYNTEVQEEDKPVVDFLYNLYLQNGGKKGPPPDTHRVKALIARVKRDAARNRVKRADGSS
ATRVTATTTITPYSTAAGYIHQEAHIGDCQKQTQFCKNKNGSDVSDTEADPTYAFRDKPH
DHDTACKC

Sequence of entity 2 (B), FASTA

>5MZA_2 Intercellular adhesion molecule 1 (chains B)
QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQED
SQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLT
VVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPY
QLQTFG

Ligands and cofactors

ID	Name	Formula	Copies
3PO	Triphosphate	H5 O10 P3	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Primary citation

Structure-Guided Identification of a Family of Dual Receptor-Binding PfEMP1 that Is Associated with Cerebral Malaria. Lennartz, F., Adams, Y., Bengtsson, A. et al. Cell Host Microbe (2017) 21:403-414. DOI 10.1016/j.chom.2017.02.009 · PubMed

Browse structure collections

About this viewer

MolViewer shows 5MZA directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.