7ZLJ
Cryo-EM structure of C-mannosyltransferase CeDPY19, in ternary complex with Dol25-P-C-Man and acceptor peptide, bound to CMT2-Fab and anti-Fab nanobody
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | H | CMT2-Fab heavy chain | polymer | 236 | 25000.7 | 1 | synthetic construct | ||
| 2 | K | Anti-Fab nanobody | polymer | 123 | 13390.6 | 1 | synthetic construct | ||
| 3 | L | CMT2-Fab light chain | polymer | 215 | 23238.8 | 1 | UniProt (Q7Z3Y4) Pfam (PF07686) Pfam (PF07654) In PDB | synthetic construct | |
| 4 | A | C-mannosyltransferase dpy-19 | polymer | 707 | 80892.6 | 1 | UniProt (P34413) Pfam (PF10034) In PDB | Caenorhabditis elegans | Protein dumpy-19 |
| 5 | P | synthetic octapeptide WEHI 1886493 | polymer | 7 | 821.9 | 1 | synthetic construct | ||
| 6 | A | [(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl-[(3~{S},6~{E},10~{Z},14~{E})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphinic acid | non-polymer | 600.8 | 1 | Chemie (IZU) | |||
| 7 | water | water | 18.0 | 10 | Chemie (HOH) |
Sequence modifications
L: 2 - 215 (UniProt: Q7Z3Y4)
A: 1 - 683 (UniProt: P34413)
| PDB | External Database | Details |
|---|---|---|
| Ser 1 | - | expression tag |
| Arg 19 | Thr 40 | conflict |
| Ser 29 | Asp 50 | conflict |
| Val 30 | Ile 51 | conflict |
| Ser 32 | Asn 53 | conflict |
| Ala 33 | Tyr 54 | conflict |
| Val 34 | Leu 55 | conflict |
| Tyr 37 | Phe 58 | conflict |
| Leu 47 | Ser 68 | conflict |
| Ser 51 | Gly 72 | conflict |
| Tyr 56 | Gln 77 | conflict |
| Pro 60 | Gln 81 | conflict |
| Arg 62 | Lys 83 | conflict |
| Arg 67 | Gly 88 | conflict |
| Gly 92 | Tyr 113 | conflict |
| Ala 93 | Lys 114 | conflict |
| Glu 95 | Tyr 116 | conflict |
| Ile 97 | Val 118 | conflict |
| Val 105 | Leu 126 | conflict |
| Ser 124 | Glu 145 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Leu 684 | - | expression tag |
| Glu 685 | - | expression tag |
| Asp 686 | - | expression tag |
| Tyr 687 | - | expression tag |
| Lys 688 | - | expression tag |
| Asp 689 | - | expression tag |
| His 690 | - | expression tag |
| Asp 691 | - | expression tag |
| Gly 692 | - | expression tag |
| Asp 693 | - | expression tag |
| Tyr 694 | - | expression tag |
| Lys 695 | - | expression tag |
| Asp 696 | - | expression tag |
| His 697 | - | expression tag |
| Asp 698 | - | expression tag |
| Ile 699 | - | expression tag |
| Asp 700 | - | expression tag |
| Tyr 701 | - | expression tag |
| Lys 702 | - | expression tag |
| Asp 703 | - | expression tag |
| Asp 704 | - | expression tag |
| Asp 705 | - | expression tag |
| Asp 706 | - | expression tag |
| Lys 707 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 5 |
| Total formula weight | 143344.6 | |
| Non-Polymers* | Number of molecules | 1 |
| Total formula weight | 600.8 | |
| All* | Total formula weight | 143945.4 |
