3WYF: Xpo1p-Yrb2p-Gsp1p-GTP complex
Crystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex. Determined by X-ray diffraction at 2.22 Å resolution. Released 12 Nov 2014.
- Method
- X-ray diffraction
- Resolution
- 2.22 Å
- Organisms
- Saccharomyces cerevisiae AWRI796, Saccharomyces cerevisiae S288c
- Chains
- 6
- Atoms
- 22,420
- Mol. weight
- 344.02 kDa
- Ligands
- MG, GTP
- Released
- 12 Nov 2014
Explore 3WYF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3WYF contains 164 α-helices and 33 β-strands across 6 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: 9 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-19 | 8 | 1 |
| α-helix | 25-34 | 10 | |
| β-strand | 47-57 | 11 | 1 |
| β-strand | 59-68 | 10 | 1 |
| α-helix | 72-74 | 3 | |
| α-helix | 78-81 | 4 | |
| β-strand | 87-93 | 7 | 1 |
| α-helix | 97-101 | 5 | |
| α-helix | 103-113 | 11 | |
| β-strand | 119-124 | 6 | 1 |
| α-helix | 135-137 | 3 | |
| α-helix | 140-144 | 5 | |
| β-strand | 147-150 | 4 | 1 |
| α-helix | 161-171 | 11 | |
| β-strand | 178 | 1 | 1 |
| α-helix | 180-182 | 3 | |
Chain B: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 103-104 | 2 | |
| α-helix | 147-149 | 3 | |
| α-helix | 152-154 | 3 | |
| β-strand | 213-225 | 13 | 2 |
| β-strand | 232-244 | 13 | 2 |
| β-strand | 252-257 | 6 | 2 |
| β-strand | 264-270 | 7 | 2 |
| β-strand | 276-278 | 3 | 2 |
| α-helix | 286-288 | 3 | |
| β-strand | 289-293 | 5 | 2 |
| β-strand | 303-307 | 5 | 2 |
| α-helix | 311-322 | 12 | |
Chain C: 70 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1-5 | 5 | |
| α-helix | 13-25 | 13 | |
| α-helix | 28-43 | 16 | |
| α-helix | 47-50 | 4 | |
| α-helix | 51-57 | 7 | |
| α-helix | 61-78 | 18 | |
| α-helix | 79-81 | 3 | |
| α-helix | 84-102 | 19 | |
| α-helix | 105-110 | 6 | |
| α-helix | 112-129 | 18 | |
| α-helix | 137-144 | 8 | |
| α-helix | 149-163 | 15 | |
| α-helix | 164-168 | 5 | |
| α-helix | 176-203 | 28 | |
| α-helix | 207-220 | 14 | |
| α-helix | 227-230 | 4 | |
| α-helix | 234-239 | 6 | |
| α-helix | 241-244 | 4 | |
| α-helix | 249-261 | 13 | |
| α-helix | 269-285 | 17 | |
| α-helix | 286-290 | 5 | |
| α-helix | 297-303 | 7 | |
| α-helix | 308-331 | 24 | |
| α-helix | 334-336 | 3 | |
| α-helix | 337-350 | 14 | |
| α-helix | 356-375 | 20 | |
| α-helix | 414-417 | 4 | |
| α-helix | 421-433 | 13 | |
| α-helix | 435-438 | 4 | |
| β-strand | 443-445 | 3 | 3 |
| β-strand | 451-453 | 3 | 3 |
| α-helix | 459-478 | 20 | |
| α-helix | 480-495 | 16 | |
| α-helix | 502-514 | 13 | |
| α-helix | 521-541 | 21 | |
| α-helix | 545-561 | 17 | |
| α-helix | 563-567 | 5 | |
| α-helix | 570-583 | 14 | |
| α-helix | 589-606 | 18 | |
| α-helix | 608-611 | 4 | |
| α-helix | 613-614 | 2 | |
| α-helix | 621-627 | 7 | |
| α-helix | 629-632 | 4 | |
| α-helix | 638-652 | 15 | |
| α-helix | 658-668 | 11 | |
| α-helix | 670-685 | 16 | |
| α-helix | 687-691 | 5 | |
| α-helix | 693-713 | 21 | |
| α-helix | 714-717 | 4 | |
| α-helix | 718-746 | 29 | |
| α-helix | 748-752 | 5 | |
| α-helix | 754-776 | 23 | |
| α-helix | 780-782 | 3 | |
| α-helix | 783-788 | 6 | |
| α-helix | 789-801 | 13 | |
| α-helix | 804-806 | 3 | |
| α-helix | 809-822 | 14 | |
| α-helix | 823-825 | 3 | |
| α-helix | 827-845 | 19 | |
| α-helix | 853-869 | 17 | |
| α-helix | 872-875 | 4 | |
| α-helix | 879-894 | 16 | |
| α-helix | 898-917 | 20 | |
| α-helix | 922-944 | 23 | |
| α-helix | 949-951 | 3 | |
| α-helix | 952-967 | 16 | |
| α-helix | 978-980 | 3 | |
| α-helix | 987-1002 | 16 | |
| α-helix | 1008-1021 | 14 | |
| α-helix | 1025-1038 | 14 | |
| α-helix | 1046-1050 | 5 | |
| α-helix | 1051-1073 | 23 | |
Chain D: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-19 | 8 | 4 |
| α-helix | 25-34 | 10 | |
| β-strand | 47-57 | 11 | 4 |
| β-strand | 59-68 | 10 | 4 |
| α-helix | 72-74 | 3 | |
| α-helix | 78-82 | 5 | |
| β-strand | 87-93 | 7 | 4 |
| β-strand | 96 | 1 | 4 |
| α-helix | 97-101 | 5 | |
| α-helix | 103-111 | 9 | |
| β-strand | 119-124 | 6 | 4 |
| α-helix | 135-137 | 3 | |
| α-helix | 140-144 | 5 | |
| β-strand | 147-150 | 4 | 4 |
| α-helix | 161-171 | 11 | |
| β-strand | 178 | 1 | 4 |
| α-helix | 180-182 | 3 | |
| α-helix | 210-211 | 2 | |
Chain E: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 103-104 | 2 | |
| α-helix | 152-154 | 3 | |
| β-strand | 212-225 | 14 | 5 |
| β-strand | 232-245 | 14 | 5 |
| β-strand | 252-257 | 6 | 5 |
| β-strand | 264-269 | 6 | 5 |
| β-strand | 276-278 | 3 | 5 |
| α-helix | 286-288 | 3 | |
| β-strand | 289-293 | 5 | 5 |
| β-strand | 303-307 | 5 | 5 |
| α-helix | 311-322 | 12 | |
Chain F: 66 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1-5 | 5 | |
| α-helix | 13-25 | 13 | |
| α-helix | 28-43 | 16 | |
| α-helix | 47-50 | 4 | |
| α-helix | 51-57 | 7 | |
| α-helix | 61-78 | 18 | |
| α-helix | 79-81 | 3 | |
| α-helix | 84-102 | 19 | |
| α-helix | 105-110 | 6 | |
| α-helix | 112-129 | 18 | |
| α-helix | 137-145 | 9 | |
| α-helix | 149-163 | 15 | |
| α-helix | 164-168 | 5 | |
| α-helix | 176-188 | 13 | |
| α-helix | 190-203 | 14 | |
| α-helix | 207-220 | 14 | |
| α-helix | 227-230 | 4 | |
| α-helix | 234-239 | 6 | |
| α-helix | 241-244 | 4 | |
| α-helix | 249-259 | 11 | |
| α-helix | 269-285 | 17 | |
| α-helix | 286-290 | 5 | |
| α-helix | 297-302 | 6 | |
| α-helix | 308-331 | 24 | |
| α-helix | 334-336 | 3 | |
| α-helix | 337-350 | 14 | |
| α-helix | 356-375 | 20 | |
| α-helix | 414-420 | 7 | |
| α-helix | 421-433 | 13 | |
| β-strand | 443-445 | 3 | 6 |
| β-strand | 451-453 | 3 | 6 |
| α-helix | 459-478 | 20 | |
| α-helix | 480-495 | 16 | |
| α-helix | 502-514 | 13 | |
| α-helix | 521-541 | 21 | |
| α-helix | 545-561 | 17 | |
| α-helix | 563-568 | 6 | |
| α-helix | 570-583 | 14 | |
| α-helix | 589-606 | 18 | |
| α-helix | 608-611 | 4 | |
| α-helix | 621-627 | 7 | |
| α-helix | 629-632 | 4 | |
| α-helix | 638-652 | 15 | |
| α-helix | 658-668 | 11 | |
| α-helix | 670-685 | 16 | |
| α-helix | 696-713 | 18 | |
| α-helix | 714-717 | 4 | |
| α-helix | 718-741 | 24 | |
| α-helix | 754-776 | 23 | |
| α-helix | 780-782 | 3 | |
| α-helix | 783-788 | 6 | |
| α-helix | 789-801 | 13 | |
| α-helix | 804-806 | 3 | |
| α-helix | 810-822 | 13 | |
| α-helix | 823-825 | 3 | |
| α-helix | 827-843 | 17 | |
| α-helix | 853-869 | 17 | |
| α-helix | 872-875 | 4 | |
| α-helix | 879-894 | 16 | |
| α-helix | 898-917 | 20 | |
| α-helix | 922-944 | 23 | |
| α-helix | 949-951 | 3 | |
| α-helix | 952-967 | 16 | |
| α-helix | 978-980 | 3 | |
| α-helix | 987-1002 | 16 | |
| α-helix | 1008-1021 | 14 | |
| α-helix | 1025-1038 | 14 | |
| α-helix | 1046-1050 | 5 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Gsp1p | A, D | protein | 219 | Saccharomyces cerevisiae AWRI796 | P32835 (AlphaFold model) |
| Ran-specific GTPase-activating protein 2 | B, E | protein | 238 | Saccharomyces cerevisiae S288c | P40517 (AlphaFold model) |
| Exportin-1 | C, F | protein | 1049 | Saccharomyces cerevisiae S288c | P30822 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>3WYF_1 Gsp1p (chains A, D)
MSAPAANGEVPTFKLVLVGDGGTGKTTFVKRHLTGEFEKKYIATIGVEVHPLSFYTNFGE
IKFDVWDTAGLEKFGGLRDGYYINAQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIV
LCGNKVDVKERKVKAKTITFHRKKNLQYYDISAKSNYNFEKPFLWLARKLAGNPQLEFVA
SPALAPPEVQVDEQLMQQYQQEMEQATALPLPDEDDADL
Sequence of entity 2 (B, E), FASTA
>3WYF_2 Ran-specific GTPase-activating protein 2 (chains B, E)
EDDKKEDKFVFGAASKFGTGFGVAKKDTKDGDATTSTESLPASDSKTKKPFAFGSGLSFG
SGFNILKNKTENNSESEKKATDVDKDKVHSGSEQLANASEDTKDKPKPLKLQKQEVKSGE
ESEECIYQVNAKLYQLSNIKEGWKERGVGIIKINKSKDDVEKTRIVMRSRGILKVILNIQ
LVKGFTVQKGFTGSLQSEKFIRLLAVDDNGDPAQYAIKTGKKETTDELYNIIVKSVPK
Sequence of entity 3 (C, F), FASTA
>3WYF_3 Exportin-1 (chains C, F)
GAMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFS
TNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKS
DLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAK
ALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILELL
STKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLK
ATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEEREL
FKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEVLVVENDEGEIVREF
VKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSI
SGTMSEDTEKRFVVTVIKDLLDLTVKKRGKDNKAVVASDIMYVVGQYPRFLKAHWNFLRT
VILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTAD
LQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSET
VKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPK
VRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCM
TTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFL
ELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIF
VSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYL
ANMLSNAFPHLTSEQIASFLSALTKQYKDLVVFKGTLRDFLVQIKEVGGDPTDYLFAEDK
ENALMEQNRLEREKAAKIGGLLKPSELDD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 2 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 2 |
Primary citation
Structural insights into how yrb2p accelerates the assembly of the xpo1p nuclear export complex. Koyama, M., Shirai, N., Matsuura, Y. Cell Rep (2014) 9:983-995. DOI 10.1016/j.celrep.2014.09.052 · PubMed
Other PDB entries of the same protein (UniProt P32835 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3M1I 2.0 Å, Crystal structure of yeast CRM1 (Xpo1p) in complex with yeast RanBP1 (Yrb1p) and yeast…
- 3WYG 2.15 Å, Crystal structure of Xpo1p-PKI-Gsp1p-GTP complex
- 5XOJ 2.2 Å, Crystal structure of Xpo1p-PKI-Nup42p-Gsp1p-GTP complex
- 2X19 2.8 Å, Crystal structure of Importin13 - RanGTP complex
- 9B3I 2.88 Å, Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114-RanGTP
- 8QYZ 3.0 Å, Crystal structure of hiNES2 in complex with Xpo1 and RanGTP
- 9D45 3.1 Å, Cryo-EM structure of yeast Exportin Msn5 bound to cargo Pho4 and RanGTP
- 9DZ6 3.1 Å, Cryo-EM structure of yeast Exportin Msn5 bound to RanGTP and Pho4 (not modeled) (State…
- 3ICQ 3.2 Å, Karyopherin nuclear state
- 9DXM 3.2 Å, Cryo-EM structure of yeast Exportin Msn5 bound to RanGTP and Pho4 (not modeled) (State…
- 9OGB 3.25 Å, Cryo-EM structure of human exportin-1 conjugated with selinexor and bound to yeast…
- 8F1E 3.28 Å, Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B
Browse structure collections
About this viewer
MolViewer shows 3WYF 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.