Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase

2024-03-13 REL RCSB RCSB RCSB 2016-10-12 2016-10-26 2016-10-26 2024-03-13 Canadian Institutes of Health Research (CIHR) MOP81294 Canada Wellcome Trust WT008150 United Kingdom Wellcome Trust WT099141 United Kingdom European Research Council (ERC) ERC268851 European Union Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Mazhab-Jafari MT Rohou A Schmidt C Bueler SA Benlekbir S Robinson CV Rubinstein JL Rotary ATPase, Vacuolar-type ATPase, Electron Cryomicroscopy, Vo region, Membrane protein, MOTOR PROTEIN Mazhab-Jafari MT Rohou A Schmidt C Bueler SA Benlekbir S Robinson CV Rubinstein JL Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase. Nature UK 539 118 122 2016 27776355 doi:10.1038/nature19828 1476-4687 0006 NATUAS 5tj5 FULLOVERLAP Vo region of the V-ATPase from Saccharomyces cerevisiae Vo region of the V-ATPase from Saccharomyces cerevisiae 0 1 2 3 4 5 6 7 8 Saccharomyces cerevisiae 0.3 V-type proton ATPase subunit a Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.070067984 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)AQYREINAGLPTIVTFPFMFAIMFGDMGHG FLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYNDIFSKTMTIFKSGWKWPDHWKKGESITAT SVGTYPIGLDWAWHGTENALLFSNSYKMKLSILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVC IVYKWAVDWVKDGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTHKKKSHEPLP STEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTIEFCLNCVSHTASYLRLWALSLAHAQLSSV LWTMTIQIAFGFRGFVGVFMTVALFAMWFALTCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEV P32563 V-type proton ATPase subunit c'' Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.022610640999999997 1 LEVO MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWANLGIALCVGLSVVGAAWGIF ITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIVFSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICG IAVGITGATAAISDAADSALFVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ P23968 V-type proton ATPase subunit c' Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.015195271 1 LEVO FFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSLIPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGF MHLSCGLCVGFACLSSGYAIGMVGDVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGS P32842 V-type proton ATPase subunit c Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.015218086999999998 8 LEVO APFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGF IQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDV P25515 V-type proton ATPase subunit e Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.006476928 1 LEVO YTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLVA Q3E7B6 V-type proton ATPase subunit f Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.0046136779999999995 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) V-type proton ATPase subunit d Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.032854237999999994 1 LEVO VYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSSESLTTSLIQEYASSKLYHEFNYI RDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDKGEILQRCHPLGWFDTLPTLSVATDLESLYETVLVD(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)NIEIIRNKLYKAYLEDFYNFVTEEIP(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)LEDHFYQLEMELCRDAFTQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNY P32366 P32366 P32366 singleParticle particle 2.5 7.5

50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin

Maxtaform COPPER/RHODIUM 400 HOLEY GLOW DISCHARGE 15 AIR ETHANE-PROPANE 100 277.3 FEI VITROBOT MARK III

Modified for ethane/propane.

The Vo region was solubilized in amphipol A8-35 (Anatrace)

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 3.4 37000.0 64350.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN

70 micro meter objective aperture, illuminated area of 1.58 micro meter diameter

GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1 4365 21.0 100.0 1

Images were recorded in "super-resolution" mode and then resampled by Fourier cropping.

657975

An in-house map of the Vo region.

C1 FOURIER SPACE 3.9 FSC 0.143 CUT-OFF FREALIGN 9.11

Data beyond 6 A resolution were omitted from refinement.

462842 PROJECTION MATCHING Weighted correlation coefficient 3.4 FREALIGN 9.11

Frealign exhaustive search (mode 3; i.e. projection matching followed by local refinement of top solutions)

PROJECTION MATCHING Weighted correlation coefficient FREALIGN 9.11

Refinement with Frealign mode 1.

emd_8409.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 310.8 310.8 310.8 90.0 90.0 90.0 X Y Z -0.15724738 0.27012172 -0.0014383988 0.010948882 1.5539999 1.5539999 1.5539999 0.0475 EMDB ::::EMDATABANK.org::::EMD-8409:::: Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase OTHER

phenix.real_space_refine REFINEMENT TARGET: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) MODEL TO MAP FIT. CC(ACROSS WHOLE MAP VOLUME): 0.6772 CC(ONLY ACROSS ATOMS IN THE MODEL): 0.6842

REAL