2024-05-15 REL PDBe RCSB PDBe 2016-04-28 2016-05-25 2016-06-15 2024-05-15 Structure of the S. cerevisiae alpha-mannosidase 1 Schneider S Kosinski J tetramer, cvt cargo, mannosidase, selective autophagy, hydrolase Bertipaglia C Schneider S Jakobi AJ Tarafder AK Bykov YS Picco A Kukulski W Kosinski J Hagen WJ Ravichandran AC Wilmanns M Kaksonen M Briggs JA Sachse C Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle. Embo Rep. UK 17 1044 1060 2016 27266708 doi:10.15252/embr.201541960 1469-3178 5jm0 FULLOVERLAP Alpha-mannosidase 1 Alpha-mannosidase 1 0 1
His-tagged
Saccharomyces cerevisiae S288c cytoplasm, vacuole 0.5 Alpha-mannosidase,Alpha-mannosidase,Alpha-mannosidase Saccharomyces cerevisiae S288c 0.125764156
The coordinate model contains a poly-alanine stretch that corresponds to residues 17-27 in the template sequence.
1 Komagataella pastoris LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)MSSEDIIYDPQFKPV QGIYENRLRQFIDTGGDYHDLNLPKFYDKKRISLDHDHVKVWWYQVSFERGSSPVSPDKRPSWKSIIERDKKGELEFREA NINQPFGPSWSTTWFKVKISLPEDWVKSNEQLLFQWDCSNEGIVIDPKTLIPVTAFSGGERTEYVLPKTSDGKHFFYIEA GNNGMFGCGAGSTINPPDDNRFFHLRKADIVWPDLDARALYIDFWMLGDAARELPGDSWQKHQARQLGNAVMNLFDPNDR SSVRKCRELLQREYFDSFLESSKVYEQGESQVLTNVYGIGNCHIDTAWLWPFAETRRKIVRSWSSQCTLMDRFPEYKFVA SQAQQFKWLLEDHPEFFNKVLIPKIQQSQFFAVGGTWVENDTNIPSGESLARQFFFGQRFFLKHFGLKSKIFWLPDTFGY SSQMPQLCRLSGIDKFLTQKLSWNNINSFPHSTFNWAGIDGSQLLTHMPPGNTYTADSHFGDVLRTAKQNKTPEYYGSGL MLYGKGDGGGGPTEEMLQKMRRIRSMNNRNGNVIPKLQVGITVDEFYDDILKRTNQGHDLPTWSGELYFEFHRGTYTSQA QTKKLMRLSEIKLHDLEWIAAKTSVLYPDSYKYPSKQINELWENVLLCQFHDVLPGSCIEMVYKYEAVPMLHNVVKECTS LIDKTVQFLQSQSKADLVEMRTLTWSKPEKVSEECSLNGSYTSSVTGYDDYIVLANGKLKVIICKKTGVITSITDETLGV EYLDTEHGRNKLGANQFVIYDDKPLGWQAWDTELYSVNQYKYVTKPKKVQVSCNTKEKCAVEVIFQISEKCKIKSVISLN ATAVTDAKLSKVDISTTVENWDARNKFLKVEFPVNIRNDFASYETQFGITKRPTHYNTSWDVAKFEVCHHKFADYSEYSK GVSILNDCKYGFSTHGNLMRLSLLRSPKAPDAHADMGTHEIKYAIYPHRGALSSDTVKLAHEFNYCFKYKLPKDIGMNFD DIISISGDENVILSNIKRGEDDSAVKSNYSLNPRDEQSIVVRVYESLGGESFASLNTTLNLKRIEKVDNLEMKVYKSLTA TRDESNHAINRIPIKLRPFEIASFRLYF P22855 3.2.1.24 singleParticle particle 0.4 7.5 50.0 Tris-HCl 175.0 NaCl Sodium chloride 75.0 Imidazole Imidazole Quantifoil R2/2 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR 4.5 ETHANE 95 293 FEI VITROBOT MARK III
2.5 ul of sample was applied, offset -3, 9s blotting time.
single particles alongside chains of tetramers
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 5.0 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON II (4k x 4k) INTEGRATING 1-7 1 1735 1.6 58.0
The first six frames comprised each 7 e/A2 and the final frame consequently received 16 e/A2 dose. Relion's particle polishing procedure was used.
 1 85274 73 55
EMAN2
 2 D2 FOURIER SPACE 6.3 FSC 0.143 CUT-OFF RELION 1.3
1. From 85274 initially auto-picked particles, 16678 were eliminated after 2D classification. 2. From 68596, two classes making up 33588 particles were included in the final reconstruction.
33588 PROJECTION MATCHING EMAN 2.06 PROJECTION MATCHING RELION 1.3 10 RELION 1.3 emd_8166.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 270.0 270.0 270.0 90.0 90.0 90.0 X Y Z -0.032903958 0.13467872 0.0019863124 0.010677306 1.08 1.08 1.08 0.064 AUTHOR None FLEXIBLE FIT
1. Fitting of a homology model based on PDB 2wyh combined with a homology model based on PDB 2xbz and 3cmg for the C- (residues 287-1083) and N-terminal part (residues 45-203) respectively 2. ab initio modelling for a three-helix bundle of the N-terminal part (residues 209-286) 3. creating an ideal poly-alanine helix for residues 17-27
Cross-correlation coefficient REAL 80.0