Structure of the PfEMP1 IT4var13 DBLbeta domain bound to ICAM-1. Determined by X-ray diffraction at 3.67 Å resolution. Released 25 Sept 2019.
Explore 6S8U in 3D Show helices and sheets RCSB PDB PDBe
6S8U contains 23 α-helices and 29 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 742-746 | 5 | |
| α-helix | 748-764 | 17 | |
| α-helix | 769-771 | 3 | |
| α-helix | 775-777 | 3 | |
| β-strand | 780 | 1 | 1 |
| β-strand | 783 | 1 | 1 |
| α-helix | 792-794 | 3 | |
| β-strand | 802 | 1 | 2 |
| α-helix | 826-828 | 3 | |
| β-strand | 829-830 | 2 | 3 |
| β-strand | 842-843 | 2 | 3 |
| α-helix | 845-848 | 4 | |
| α-helix | 853-856 | 4 | |
| β-strand | 858 | 1 | 2 |
| α-helix | 860-864 | 5 | |
| α-helix | 869-895 | 27 | |
| α-helix | 904-925 | 22 | |
| α-helix | 934-953 | 20 | |
| α-helix | 978-1000 | 23 | |
| α-helix | 1008-1010 | 3 | |
| α-helix | 1020-1022 | 3 | |
| α-helix | 1025-1052 | 28 | |
| α-helix | 1067-1106 | 40 | |
| β-strand | 1112-1114 | 3 | 4 |
| α-helix | 1120-1133 | 14 | |
| α-helix | 1145-1147 | 3 | |
| α-helix | 1149-1155 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-5 | 4 | 5 |
| β-strand | 8-12 | 5 | 4 |
| β-strand | 15-23 | 9 | 5 |
| β-strand | 31-34 | 4 | 6 |
| β-strand | 41-42 | 2 | 5 |
| β-strand | 49-57 | 9 | 5 |
| β-strand | 61 | 1 | 4 |
| β-strand | 64-67 | 4 | 6 |
| β-strand | 74-77 | 4 | 6 |
| β-strand | 79-83 | 5 | 4 |
| β-strand | 84 | 1 | 7 |
| β-strand | 88-91 | 4 | 8 |
| α-helix | 92-93 | 2 | |
| β-strand | 97-99 | 3 | 9 |
| β-strand | 103-111 | 9 | 8 |
| β-strand | 114 | 1 | 7 |
| α-helix | 116-118 | 3 | |
| β-strand | 119-125 | 7 | 10 |
| β-strand | 128-134 | 7 | 10 |
| β-strand | 140-147 | 8 | 8 |
| α-helix | 150-152 | 3 | |
| β-strand | 156-164 | 9 | 10 |
| β-strand | 172-176 | 5 | 10 |
| β-strand | 180-181 | 2 | 10 |
| β-strand | 183-185 | 3 | 9 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Erythrocyte membrane protein 1 | A | protein | 469 | Plasmodium falciparum | E0A3B3 |
| Intercellular adhesion molecule 1 | B | protein | 186 | Homo sapiens | P05362 (AlphaFold model) |
>6S8U_1 Erythrocyte membrane protein 1 (chains A) PCVVGGQADTIYPAIANQMAHQMHEDAQTEASKRGLAKLRADAKQGIYKKNRKPQELSNI CNITLQHSNDSRNGNNGGACTGKDGNNERFKIGTEWKIGEKVETTDTDAYIPPRRQHMCT SNLENLNVSWVTEDGKAIHSLLGDVQLAAKMDADEIIKRYKKHNTLTDPIQQKDQESICR AVRYSFADLGDIIRGRDLWEHGDQTKLQGHLQIIFGKIKEEIKKKHPGINGNDKYKGDEK NNPPYKQLREDWWEANRHQVWRAMQCELKNLKKSNGDCHYNSRGTPLDDYIPQRLRWMVE WAEWFCKMQSQEYDKLMKQCSQCMSKGGDCRKGDVNCTSCEQACEEYKKKIKKWEKQWNK IKDKYEELYLQAKIAFAGTSFGGGDRDYQQMVHFFKELQKVTGDTTLGDTTSPYSTAAGY IHQEGHVDECTEQTQFCKNRNGNTASGKEDDNYTFKDPPPKYANACKCD
>6S8U_2 Intercellular adhesion molecule 1 (chains B) QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQED SQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLT VVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPY QLQTFG
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
Structural insights into diverse modes of ICAM-1 binding byPlasmodium falciparum-infected erythrocytes. Lennartz, F., Smith, C., Craig, A.G. et al. Proc Natl Acad Sci U S A (2019) 116:20124-20134. DOI 10.1073/pnas.1911900116 · PubMed
Other PDB entries of the same protein (UniProt E0A3B3), best resolution first:
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