2024-03-06 REL RCSB RCSB RCSB 2020-03-30 2020-04-08 2020-08-19 2024-03-06 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM108753 United States Asymmetric vertex of the clathrin minicoat cage, subparticle refinement of the clathrin layer Paraan M Mendez J Sharum S Kurtin D He H Stagg S Clathrin coated vesicle, clathrin heavy chain, clathrin light chain, clathrin cage, ENDOCYTOSIS Paraan M Mendez J Sharum S Kurtin D He H Stagg SM The structures of natively assembled clathrin-coated vesicles. Sci Adv US 6 eaba8397 eaba8397 2020 32743076 doi:10.1126/sciadv.aba8397 2375-2548 EMD-21608 other EM volume EMD-21609 other EM volume EMD-21610 other EM volume EMD-21612 other EM volume EMD-21613 other EM volume EMD-21614 other EM volume EMD-21616 other EM volume EMD-21615 other EM volume 6wcj FULLOVERLAP Natively assembled clathrin coated vesicles Natively assembled clathrin coated vesicles 0 1 2 Bos taurus brain Clathrin heavy chain 1 Bos taurus 0.191800312 9 LEVO MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVI ALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDA KQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGN QPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNR KGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGAEELFARKFNALFAQGNYSEAAKVAANAPKGILRTPDTIRR FQSVPAQPGQTSPLLQYFGILLDQGQLNKYESLELCRPVLQQGRKQLLEKWLKEDKLECSEELGDLVKSVDPTLALSVYL RANVPNKVIQCFAETGQVQKIVLYAKKVGYTPDWIFLLRNVMRISPDQGQQFAQMLVQDEEPLADITQIVDVFMEYNLIQ QCTAFLLDALKNNRPSEGPLQTRLLEMNLMHAPQVADAILGNQMFTHYDRAHIAQLCEKAGLLQRALEHFTDLYDIKRAV VHTHLLNPEWLVNYFGSLSVEDSLECLRAMLSANIRQNLQICVQVASKYHEQLSTQSLIELFESFKSFEGLFYFLGSIVN FSQDPDVHFKYIQAACKTGQIKEVERICRESNCYDPERVKNFLKEAKLTDQLPLIIVCDRFDFVHDLVLYLYRNNLQKYI EIYVQKVNPSRLPVVIGGLLDVDCSEDVIKNLILVVRGQFSTDELVAEVEKRNRLKLLLPWLEARIHEGCEEPATHNALA KIYIDSNNNPERFLRENPYYDSRVVGKYCEKRDPHLACVAYERGQCDLELINVCNENSLFKSLSRYLVRRKDPELWGSVL LESNPYRRPLIDQVVQTALSETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKADRTRV MEYINRLDNYDAPDIANIAISNELFEEAFAIFRKFDVNTSAVQVLIEHIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGM VKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQ VGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHA DELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAE LVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFKPLLLNDLLMVLSPRLDHTRAVNYFS KVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLEKHELIEFRRIAAYLFKGNNR WKQSVELCKKDSLYKDAMQYASESKDTELAEELLQWFLQEEKRECFGACLFTCYDLLRPDVVLETAWRHNIMDFAMPYFI QVMKEYLTKVDKLDASESLRKEEEQATETQPIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGYSM P49951 Clathrin light chain B Bos taurus 0.025109396 6 LEVO MADDFGFFSSSESGAPEAAEEDPAAAFLAQQESEIAGIENDEGFGAPAGSQGGLAQPGPASGASEDMGATVNGDVFQEAN GPADGYAAIAQADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAF YQQPDADIIGYVASEEAFVKESKEETPGTEWEKVAQLCDFNPKSSKQCKDVSRLRSVLMSLKQTPLSR P04975 singleParticle particle 6 6.7 100.0 MES 1.0 MgCl2 Magnesium Chloride 1.0 EGTA C-flat-2/2 4C ETHANE 100 281 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 3.0 5.0 35000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 800 50.0 1 360000
These are subparticle images that were extracted from particle images. Each minicoat particle has 24 asymmetric vertices. From a total of 15000 minicoat particles, 360000 vertex subparticles were extracted. The position of subparticles was calculated by the localized reconstruction script in scipion, and the subparticle images were extracted with RELION extraction tools.
An asymmetric vertex was cut out of the minicoat cage map from the same dataset.
 C1 6.3 FSC 0.143 CUT-OFF cisTEM 1
After the final refinement in cisTEM, half-maps were generated in cisTEM and the FSC was calculated with EMAN FSC tools.
305413 OTHER cryoSPARC 2
Using the Euler angles of the mini-coat cage particles and the position of the pentagonal faces in the map, initial hexagonal face Eulers were calculated. Using 2D classification and homogenous refinement tools of cryoSPARC shifts, Euler angles were refined for binned-by-2 subparticle images.
 PROJECTION MATCHING cisTEM 1 RELION 3
The output of cryoSPARC was imported into cisTEM for unbinned refinement. Then, the initial output of cisTEM was used for RELION's per particle defocus estimation and beam tilt estimation. This was done step-by-step and after each estimation the map was refined in RELION. After defocus and beam tilt estimation with RELION converged, the vertex map was refined in cisTEM one last time.
 emd_21611.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 -300 -300 -300 600 600 600 793.8 793.8 793.8 90.0 90.0 90.0 X Y Z -9.133832999999999 19.386827 0.008423435 0.23832925 1.323 1.323 1.323 4.0 AUTHOR Sharpened asymmetric vertex 6SCT A 1627-1641 PDB experimental model 6SCT C 1627-1641 PDB experimental model 6SCT D 1627-1641 PDB experimental model AB INITIO MODEL 6SCT B 188-228 PDB experimental model 6SCT E 188-228 PDB experimental model 6SCT F 188-228 PDB experimental model AB INITIO MODEL 6SCT A 1248-1626 PDB experimental model 6SCT C 1248-1626 PDB experimental model 6SCT D 1248-1626 PDB experimental model 6SCT B 99-166 PDB experimental model 6SCT E 99-166 PDB experimental model 6SCT F 99-166 PDB experimental model 6SCT O PDB experimental model 6SCT L PDB experimental model 6SCT M PDB experimental model 6SCT J PDB experimental model 6SCT G PDB experimental model 6SCT H PDB experimental model 6SCT N PDB experimental model 6SCT I PDB experimental model 6SCT K PDB experimental model FLEXIBLE FIT emd_21611_msk_1.map emd_21611_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 -300 -300 -300 600 600 600 793.8 793.8 793.8 90.0 90.0 90.0 X Y Z -7.1984806 16.155186 0.017947992 0.5891118 1.323 1.323 1.323 AUTHOR Nonsharpened asymmetric vertex emd_21611_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 -300 -300 -300 600 600 600 793.8 793.8 793.8 90.0 90.0 90.0 X Y Z -8.194691000000001 11.410598999999999 -0.022753386 0.53686446 1.323 1.323 1.323 AUTHOR Unmasked half map emd_21611_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 -300 -300 -300 600 600 600 793.8 793.8 793.8 90.0 90.0 90.0 X Y Z -8.258146 10.746693 -0.023451688 0.5363368 1.323 1.323 1.323 AUTHOR Unmasked half map