6F0X: TRIP13
Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20. Determined by electron microscopy at 4.6 Å resolution. Released 2 May 2018.
- Method
- Electron microscopy
- Resolution
- 4.6 Å
- Organism
- Homo sapiens
- Chains
- 9
- Atoms
- 20,450
- Mol. weight
- 403.67 kDa
- Ligands
- AGS
- Released
- 2 May 2018
Explore 6F0X in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6F0X contains 106 α-helices and 85 β-strands across 9 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: 13 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 123-126 | 4 | 1 |
| α-helix | 130-132 | 3 | |
| α-helix | 145-160 | 16 | |
| β-strand | 174-178 | 5 | 1 |
| α-helix | 185-199 | 15 | |
| β-strand | 206-211 | 6 | 1 |
| α-helix | 214-217 | 4 | |
| α-helix | 222-240 | 19 | |
| β-strand | 245-251 | 7 | 1 |
| α-helix | 254-256 | 3 | |
| α-helix | 274-288 | 15 | |
| β-strand | 295-298 | 4 | 1 |
| β-strand | 317-318 | 2 | 1 |
| α-helix | 324-340 | 17 | |
| α-helix | 353-358 | 6 | |
| α-helix | 368-378 | 11 | |
| α-helix | 385-394 | 10 | |
| α-helix | 395-400 | 6 | |
| α-helix | 409-427 | 19 | |
Chain B: 19 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-27 | 5 | 2 |
| α-helix | 35-49 | 15 | |
| β-strand | 57-58 | 2 | 2 |
| α-helix | 64-69 | 6 | |
| β-strand | 72-75 | 4 | 2 |
| β-strand | 97-101 | 5 | 2 |
| β-strand | 123-126 | 4 | 3 |
| α-helix | 130-132 | 3 | |
| α-helix | 135-138 | 4 | |
| α-helix | 145-162 | 18 | |
| β-strand | 174-178 | 5 | 3 |
| α-helix | 185-199 | 15 | |
| β-strand | 208-212 | 5 | 3 |
| α-helix | 214-217 | 4 | |
| α-helix | 224-241 | 18 | |
| β-strand | 247-253 | 7 | 3 |
| α-helix | 254-256 | 3 | |
| α-helix | 259-261 | 3 | |
| α-helix | 268-287 | 20 | |
| β-strand | 293-299 | 7 | 3 |
| α-helix | 302-304 | 3 | |
| α-helix | 308-311 | 4 | |
| β-strand | 315-318 | 4 | 3 |
| α-helix | 324-340 | 17 | |
| β-strand | 344 | 1 | 4 |
| α-helix | 353-358 | 6 | |
| α-helix | 368-378 | 11 | |
| α-helix | 385-395 | 11 | |
| α-helix | 396-400 | 5 | |
| β-strand | 405 | 1 | 4 |
| α-helix | 407-428 | 22 | |
Chain C: 20 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 5 |
| β-strand | 25-27 | 3 | 6 |
| α-helix | 35-49 | 15 | |
| β-strand | 57-58 | 2 | 7 |
| α-helix | 64-69 | 6 | |
| β-strand | 70 | 1 | 6 |
| β-strand | 73-74 | 2 | 7 |
| β-strand | 94-96 | 3 | 5 |
| β-strand | 99-101 | 3 | 6 |
| β-strand | 122-126 | 5 | 8 |
| α-helix | 130-132 | 3 | |
| α-helix | 135-137 | 3 | |
| α-helix | 145-160 | 16 | |
| β-strand | 174-176 | 3 | 8 |
| β-strand | 177-178 | 2 | 9 |
| α-helix | 185-199 | 15 | |
| α-helix | 200-202 | 3 | |
| β-strand | 208-212 | 5 | 8 |
| α-helix | 214-217 | 4 | |
| α-helix | 224-241 | 18 | |
| β-strand | 247-251 | 5 | 8 |
| α-helix | 254-256 | 3 | |
| α-helix | 270-287 | 18 | |
| β-strand | 294-297 | 4 | 8 |
| α-helix | 302-304 | 3 | |
| α-helix | 307-312 | 6 | |
| β-strand | 317-318 | 2 | 9 |
| α-helix | 322-323 | 2 | |
| α-helix | 324-340 | 17 | |
| β-strand | 344 | 1 | 10 |
| α-helix | 353-358 | 6 | |
| α-helix | 365-380 | 16 | |
| α-helix | 385-395 | 11 | |
| α-helix | 396-400 | 5 | |
| β-strand | 405 | 1 | 10 |
| α-helix | 410-427 | 18 | |
Chain D: 13 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 11 |
| β-strand | 24-27 | 4 | 12 |
| α-helix | 35-49 | 15 | |
| β-strand | 57-58 | 2 | 12 |
| α-helix | 64-69 | 6 | |
| β-strand | 70-74 | 5 | 12 |
| β-strand | 94-96 | 3 | 11 |
| β-strand | 99-101 | 3 | 12 |
| β-strand | 122-126 | 5 | 13 |
| α-helix | 145-158 | 14 | |
| β-strand | 174-178 | 5 | 13 |
| α-helix | 185-199 | 15 | |
| β-strand | 208-212 | 5 | 13 |
| α-helix | 214-216 | 3 | |
| α-helix | 224-241 | 18 | |
| β-strand | 247-250 | 4 | 13 |
| α-helix | 255-258 | 4 | |
| α-helix | 268-287 | 20 | |
| β-strand | 293-297 | 5 | 13 |
| β-strand | 315-318 | 4 | 13 |
| α-helix | 324-340 | 17 | |
| α-helix | 353-358 | 6 | |
| α-helix | 368-380 | 13 | |
| α-helix | 385-399 | 15 | |
| α-helix | 410-428 | 19 | |
Chain E: 16 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 25 | 1 | 14 |
| β-strand | 26-27 | 2 | 15 |
| α-helix | 35-49 | 15 | |
| β-strand | 58 | 1 | 16 |
| α-helix | 64-69 | 6 | |
| β-strand | 70-72 | 3 | 15 |
| β-strand | 73 | 1 | 16 |
| β-strand | 99 | 1 | 14 |
| β-strand | 123-126 | 4 | 17 |
| α-helix | 130-132 | 3 | |
| α-helix | 135-138 | 4 | |
| α-helix | 145-162 | 18 | |
| β-strand | 174-176 | 3 | 17 |
| β-strand | 178 | 1 | 18 |
| α-helix | 185-200 | 16 | |
| β-strand | 206-211 | 6 | 17 |
| α-helix | 226-240 | 15 | |
| β-strand | 245-251 | 7 | 17 |
| α-helix | 254-256 | 3 | |
| α-helix | 271-286 | 16 | |
| α-helix | 287-289 | 3 | |
| β-strand | 293-297 | 5 | 17 |
| β-strand | 318 | 1 | 18 |
| α-helix | 324-340 | 17 | |
| α-helix | 353-358 | 6 | |
| α-helix | 367-378 | 12 | |
| α-helix | 385-388 | 4 | |
| α-helix | 391-399 | 9 | |
| α-helix | 410-427 | 18 | |
Chain F: 14 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 123-126 | 4 | 19 |
| α-helix | 130-132 | 3 | |
| α-helix | 145-162 | 18 | |
| β-strand | 174-175 | 2 | 19 |
| β-strand | 177-178 | 2 | 20 |
| α-helix | 185-199 | 15 | |
| β-strand | 206-212 | 7 | 19 |
| α-helix | 228-240 | 13 | |
| β-strand | 245-247 | 3 | 19 |
| β-strand | 249-251 | 3 | 19 |
| α-helix | 255-258 | 4 | |
| α-helix | 274-287 | 14 | |
| β-strand | 295-297 | 3 | 19 |
| α-helix | 307-311 | 5 | |
| β-strand | 317-318 | 2 | 20 |
| α-helix | 322-323 | 2 | |
| α-helix | 324-338 | 15 | |
| α-helix | 353-358 | 6 | |
| α-helix | 368-378 | 11 | |
| α-helix | 385-395 | 11 | |
| α-helix | 396-400 | 5 | |
| α-helix | 407-423 | 17 | |
Chain P: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 56 | 1 | 21 |
| α-helix | 68-83 | 16 | |
| α-helix | 123-144 | 22 | |
| β-strand | 149-154 | 6 | 21 |
| β-strand | 163-168 | 6 | 21 |
| α-helix | 183-196 | 14 | |
| β-strand | 210-217 | 8 | 21 |
| β-strand | 227-228 | 2 | 21 |
| β-strand | 239-243 | 5 | 21 |
| α-helix | 255-258 | 4 | |
| β-strand | 261-264 | 4 | 21 |
| β-strand | 269-270 | 2 | 21 |
Chain Q: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 131-132 | 2 | 22 |
| α-helix | 134-136 | 3 | |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Pachytene checkpoint protein 2 homolog | A, B, C, D, E, F | protein | 432 | Homo sapiens | Q15645 (AlphaFold model) |
| MAD2L1-binding protein | P | protein | 274 | Homo sapiens | Q15013 (AlphaFold model) |
| Cell division cycle protein 20 homolog | Q | protein | 499 | Homo sapiens | Q12834 (AlphaFold model) |
| Mitotic spindle assembly checkpoint protein MAD2A | Z | protein | 205 | Homo sapiens | Q13257 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>6F0X_1 Pachytene checkpoint protein 2 homolog (chains A, B, C, D, E, F)
MDEAVGDLKQALPCVAESPTVHVEVHQRGSSTAKKEDINLSVRKLLNRHNIVFGDYTWTE
FDEPFLTRNVQSVSIIDTELKVKDSQPIDLSACTVALHIFQLNEDGPSSENLEEETENII
AANHWVLPAAEFHGLWDSLVYDVEVKSHLLDYVMTTLLFSDKNVNSNLITWNRVVLLHGP
PGTGKTSLCKALAQKLTIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLI
DDKDALVFVLIDQVESLTAARNACRAGTEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSN
ITEKIDVAFVDRADIKQYIGPPSAAAIFKIYLSCLEELMKCQIIYPRQQLLTLRELEMIG
FIENNVSKLSLLLNDISRKSEGLSGRVLRKLPFLAHALYVQAPTVTIEGFLQALSLAVDK
QFEERKKLAAYI
Sequence of entity 2 (P), FASTA
>6F0X_2 MAD2L1-binding protein (chains P)
MAAPEAEVLSSAAVPDLEWYEKSEETHASQIELLETSSTQEPLNASEAFCPRDCMVPVVF
PGPVSQEGCCQFTCELLKHIMYQRQQLPLPYEQLKHFYRKPSPQAEEMLKKKPRATTEVS
SRKCQQALAELESVLSHLEDFFARTLVPRVLILLGGNALSPKEFYELDLSLLAPYSVDQS
LSTAACLRRLFRAIFMADAFSELQAPPLMGTVVMAQGHRNCGEDWFRPKLNYRVPSRGHK
LTVTLSCGRPSIRTTAWEDYIWFQAPVTFKGFRE
Sequence of entity 3 (Q), FASTA
>6F0X_3 Cell division cycle protein 20 homolog (chains Q)
MAQFAFESDLHSLLQLDAPIPNAPPARWQRKAKEAAGPAPSPMRAANRSHSAGRTPGRTP
GKSSSKVQTTPSKPGGDRYIPHRSAAQMEVASFLLSKENQPENSQTPTKKEHQKAWALNL
NGFDVEEAKILRLSGKPQNAPEGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPE
IRNDYYLNLVDWSSGNVLAVALDNSVYLWSASSGDILQLLQMEQPGEYISSVAWIKEGNY
LAVGTSSAEVQLWDVQQQKRLRNMTSHSARVGSLSWNSYILSSGSRSGHIHHHDVRVAEH
HVATLSGHSQEVCGLRWAPDGRHLASGGNDNLVNVWPSAPGEGGWVPLQTFTQHQGAVKA
VAWCPWQSNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISGHGF
AQNQLVIWKYPTMAKVAELKGHTSRVLSLTMSPDGATVASAAADETLRLWRCFELDPARR
REREKASAAKSSLIHQGIR
Sequence of entity 4 (Z), FASTA
>6F0X_4 Mitotic spindle assembly checkpoint protein MAD2A (chains Z)
MALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLE
LIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKS
QKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEE
VRLRSFTTTIHKVNSMVAYKIPVND
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| AGS | Phosphothiophosphoric acid-adenylate ester | C10 H16 N5 O12 P3 S | 5 |
Primary citation
Mechanism for remodelling of the cell cycle checkpoint protein MAD2 by the ATPase TRIP13. Alfieri, C., Chang, L., Barford, D. Nature (2018) 559:274-278. DOI 10.1038/s41586-018-0281-1 · PubMed
Other PDB entries of the same protein (UniProt Q15645 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5WC2 2.5 Å, Crystal Structure of ADP-bound human TRIP13
- 5VQA 2.54 Å, Structure of human TRIP13, ATP-bound form
- 6LK0 2.6 Å, Crystal structure of human wild type TRIP13
- 5VQ9 3.02 Å, Structure of human TRIP13, Apo form
- 7L9P 3.6 Å, Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex
Browse structure collections
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