2024-05-15 REL PDBe PDBe PDBe 2018-07-31 2018-09-05 2018-09-26 2024-05-15 Medical Research Council (United Kingdom) MC_UP_1201/16 United Kingdom Wellcome Trust 207455/Z/17/Z United Kingdom Australian Research Council DP160101743 Australia National Health and Medical Research Council (Australia) APP1042082 Australia National Health and Medical Research Council (Australia) APP1058734 Australia National Health and Medical Research Council (Australia) APP1041929 Australia National Health and Medical Research Council (Australia) APP1136021 Australia Retromer-Vps5: low-resolution overview map centred on the Vps26 dimer. Kovtun O Leneva N Ariotti N Rohan TS Owen DJ Briggs JAG Collins BM retromer, endosome, sorting nexin, BAR, membrane trafficking, PROTEIN TRANSPORT Kovtun O Leneva N Bykov YS Ariotti N Teasdale RD Schaffer M Engel BD Owen DJ Briggs JAG Collins BM Structure of the membrane-assembled retromer coat determined by cryo-electron tomography. Nature UK 561 561 564 2018 30224749 doi:10.1038/s41586-018-0526-z 1476-4687 0006 NATUAS 6h7w FULLOVERLAP Retromer-Vps5 complex assembled on the membrane. Retromer-Vps5 complex assembled on the membrane. 0 1 2 3 4 5 6
Vps26/Vps35/Vps29 trimer recruited to the membrane via Vps5 PX-BAR protein.
Chaetomium thermophilum var. thermophilum DSM 1495 Vacuolar protein sorting-associated protein 26-like protein Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) DSM 1495 / CBS 144.50 / IMI 039719 0.034308449 2 Escherichia coli LEVO FSTPVDIDIVLADADKRAMVDVKLDKNRREKVPLYMDGESVKGCVTVRPKDGKRLEHTGIKVQFIGTIEMFFDRGNHYEF LSLVQELAAPGELQHPQTFDFNFKNVEKQYESYNGINVKLRYFVRVTVSRRMADVIREKDIWVYSYRIPPELNSSIKMDV GIEDCLHIEFEYSKSKYHLKDVIVGRIYFLLVRLKIKHMELSIIRRETTGVAPNQYNESETLVRFEIMDGSPSRGETIPI RLFLGGFDLTPTFRDVNKKFSTRYYLSLVLIDEDARRYFKQSEIILYRQPPE G0S0E6 Putative vacuolar protein sorting-associated protein Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) DSM 1495 / CBS 144.50 / IMI 039719 0.042060762 8 Escherichia coli LEVO ARPTFHITVGDPHKVGDLATSHIVYSVRTKTTSKAYKQPEFEVKRRYRDFLWLYNTLHSNNPGVVVPPPPEKQAVGRFES NFVESRRAALEKMLNKIAAHPTLQLDADLKLFLESESFNIDVKHKERKEPPLGESKGVFGSLGFGGGGNKFVEQDDWFHD RRVYLDALENQLKALLKAMDNMVAQRKAMAEAAADFSASLHALSTVELSPTLSGPLDALSELQLAIRDVYERQAQQDVLT FGIIIEEYIRLIGSVKQAFSQRQKAFHSWHSAESELMKKKAAQDKLLRQGKTQQDRLNQVNAEVIDAERKVHQARLLFED MGRLLRSELDRFEREKVEDFKSGVETFLESAVEAQKELIEKWETFLMQ G0SH11 Putative vacuolar protein sorting-associated protein Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) DSM 1495 / CBS 144.50 / IMI 039719 0.014897981999999999 4 Escherichia coli LEVO ARPTFHITVGDPHKVGDLATSHIVYSVRTKTTSKAYKQPEFEVKRRYRDFLWLYNTLHSNNPGVVVPPPPEKQAVGRFES NFVESRRAALEKMLNKIAAHPTLQLDADLKLFLESESFNIDVKHKERKE G0SH11 Putative vacuolar protein sorting-associated protein Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) DSM 1495 / CBS 144.50 / IMI 039719 0.025477904 2 Escherichia coli LEVO NKFVEQDDWFHDRRVYLDALENQLKALLKAMDNMVAQRKAMAEAAADFSASLHALSTVELSPTLSGPLDALSELQLAIRD VYERQAQQDVLTFGIIIEEYIRLIGSVKQAFSQRQKAFHSWHSAESELMKKKAAQDKLLRQGKTQQDRLNQVNAEVIDAE RKVHQARLLFEDMGRLLRSELDRFEREKVEDFKSGVETFLESAVEAQKELIEKWETFLMQ G0SH11 Vacuolar protein sorting-associated protein 29 Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) DSM 1495 / CBS 144.50 / IMI 039719 0.021470654 2 Escherichia coli LEVO AFLILVIGNLHIPDRALDIPPKFKKLLSPGKISQTLCLGNLTDRATYDYLRSISPDLKIVRGRMDVEATSLPLMQVVTHG SLRIGFLEGFTLVSEEPDVLLAEANKLDVDVLCWAGGSHRFECFEYMDKFFVNPGSATGAFTTDWLAEGEEVVPSFCLMD VQGISLTLYVYQLRKDENGTENVAVEKVTYTKP G0RZB5 Vacuolar protein sorting-associated protein 35 Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) DSM 1495 / CBS 144.50 / IMI 039719 0.096140016 2 Escherichia coli LEVO RLLEDALIAVRQQTAMMRKFLDTPGKLMDALKCCSTLVSELRTSSLSPKQYYELYMAVFDALRYLSAHLRENHPVNHLAD LYELVQYAGNIIPRLYLMITVGTAYMSIDGAPVKELMKDMMDMSRGVQHPVRGLFLRYYLSGQARDYLPTGDSDGPEGNL QDSINFILTNFVEMNKLWVRLQHQGHSRERDLRTQERRELQLLVGSNIVRLSQLVDLPTYRDSILGPLLEQIVQCRDILA QEYLLEVITQVFPDEYHLHTLDQFLGAVSRLNPHVNVKAIVIGMMNRLSDYAERESQNEPEEDRAKLEEEALAKLLEKTK LGQNSELEPQNGDHPDTEVSSTTDSAQAPSTADSDTTAVNGEEEPVRKRRGIPVNVPLYDIFFDQVQHLVQAQHLPIQDT IALCCSLANLSLNIYPERLDYVDGILAYALAKVKEHANSADLHSQPAQQSLLSLLQSPLRRYVSIFTALSLPTYVSLFQA QTYPTRRAIAGEIVRTLLKNQTLISTPAHLENVLEILKVLIKEGSQPPAGYPGVVQPRARPLETDETMEEQGWLARLVHL IHSDDNDTQFRLLQMTRKAYAEGNERIRTTTPPLITAGLKLARRFKAREHYDDNWSSQSSSLFKFLHSAISTLYTRVNGP GVADLCLRLFCSCGQVADMTEFEEVAYEFFAQAFTVYEESISDSKAQFQAVCVIASALHRTRNFGRENYDTLITKCAQHA SKLLRKPDQCRAVYLASHLWWATPIAARGETEDTELYRDGKRVLECLQRALRVADSCMETATSIELFVEILDRYVYYFDQ RNESVTTKYLNGLIELIHSNLAGNQQDSASVEASRKHFIQTLEMIQ G0S709 subtomogramAveraging threeDArray 1.1 7.5 20.0 C8H19KN2O5S HEPES-KOH 200.0 NaCl sodium chloride ETHANE 95 292 LEICA EM GP
The solution-assembled complex was incubated with Folch liposomes at room temperature.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 2.5 6.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 20 GATAN K2 QUANTUM (4k x 4k) SUPER-RESOLUTION 2 3.17
Tomographic tilt series were acquired with the dose-symmetric tilt-scheme (Hagen et al., J Struct Biol. 2017)
 1
After motion correction in "alignframes" (IMOD), each of the images in the tilt series was low-pass filtered according to the electron-dose acquired by the sample (Grant and Grigorieff, 2015).
C2 BACK PROJECTION 11.4 FSC 0.143 CUT-OFF 16037 71 194885 reference-free geometrical seeding alogn the surface of manually traced tubules OTHER AV3 TOM
Image processing was performed in TOM Toolbox, AV3 and Dynamo toolboxes.
 emd_0154.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 144 144 144 0 0 0 144 144 144 388.80002 388.80002 388.80002 90.0 90.0 90.0 X Y Z -0.5354475 0.764921 0.0027230864 0.058002256 2.7 2.7 2.7 0.15 AUTHOR Low-resolution overview map of retromer-Vps5 centered on the Vps26 dimer. FLEXIBLE FIT
Note that the associated PDB model was not generated by fitting into this map! It was generated by fitting into the associated local high-resolution maps and then combined. Initial global ridgid body fitting was done using Chimera, followed by MDFF within NAMD for flexible fitting. Note that side chain positions are not reliable in model generated by refinement into a map at this resolution.