2024-11-13 REL PDBj PDBj PDBj 2017-09-21 2017-12-13 2018-01-31 2024-11-13 National Science Foundation of China 31530018 China Beijing Municipal Science & Technology Commission Z161100000116034 China National Key Research and Development Program of MOST 2016YFA0501100 China National Institute of Health R01GM111128 United States Mei K Li Y exocyst, coiled-coil, EXOCYTOSIS Mei K Li Y Wang S Shao G Wang J Ding Y Luo G Yue P Liu JJ Wang X Dong MQ Wang HW Guo W Nat. Struct. Mol. Biol. US 25 139 146 2018 29335562 doi:10.1038/s41594-017-0016-2 1545-9985 5yfp FULLOVERLAP Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5A resolution Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5A resolution 0 1 2 3 4 5 6 7 8

overall map of Yeast Exocyst complex

Saccharomyces cerevisia S288c S288c cytoplasm 0.844 Exocyst complex component SEC3 Saccharomyces cerevisiae S288c S288c 0.154889547 1 LEVO MRSSKSPFKRKSHSRETSHDENTSFFHKRTISGSSAHHSRNVSQGAVPSSAPPVSGGNYSHKRNVSRASNSSQTSNFLAE QYERDRKAIINCCFSRPDHKTGEPPNNYITHVRIIEDSKFPSSRPPPDSKLENKKKRLLILSAKPNNAKLIQIHKARENS DGSFQIGRTWQLTELVRVEKDLEISEGFILTMSKKYYWETNSAKERTVFIKSLITLYIQTFEGHVPELVNWDLSLFYLDE RSYQRAVITNRPGSVSPIKSPTSNFTTNTTQSVGSVPFSAPTERTRRSETESVNPVSTPASVEYHAGMKSLNKAPYSSNS TLNEVNKRYELEQQQQQEEAELRRLEEQKRLQLQKENEMKRLEEERRIKQEERKRQMELEHQRQLEEEERKRQMELEAKK QMELKRQRQFEEEQRLKKERELLEIQRKQREQETAERLKKEEQEALAKKEEEEKSKRNKVDNESYTQEINGKVDNLLEDL NAVLAEETETTPTMQNGTYVPERSTARAHDQLKKPLNIAKVESLGGSDLNDSISLSDEIAGLNTSNLSGEDQDEKNDLSF EKGDEVRYSNNFEGEAPHVYHEVSIIQEEAPAVSQKLILPEENNESEALIESKEEIKTMENIDDEVLLEILTDINWSIED DADSMIERIDLRLAETEYLFNQNLLSLQKIGPNIRPYEDKVNDECHRIIPTLSLFLMEMSNFSNDIENVESQDNGLQVES ANKKLLWNTLDELLKTVSLDEISLNQLLECPIREKNLPWMENQLNLLLKAFQAIGSDGNEVEYNLREISGLKQRLQFYEK VTKIFLNRIVEEMQKKFSNIRGQDISHDQMIRILTTLLIFSPLILFCKEISQKSYQAIVENWNVSIQPVYMELWTKKISQ LQGIDTNDEKMNELSLSQLLNEWDTFRKERKTNDINPVFKNSFSLLTECLQTMRQECIVYQNFVEVFFHISSKHNFEEYI KHFNDPDAPPILLDTVKVMQSDREAAVIETQLVSRIFQPIVTRLSSYFVELVKAEPTVAPALTFYLENEIKSLESSNHEF LLSAVTRMYTQIKQVWSDNVEEQVLHFERISNATTNGEILPGILDLPVGLKNSEDLFQFAKRSMDIKDTDEGYESIELMN SSFRKLSIAATRSITHKEVNSSINPNLSDTAALNNDYMETISLLVNSNWLTEMLSMLNFNKDGIFDTSLQNVKKVFDVEK ESYASFLLRDTMPKLTAFVYGVSNIIENTNNVNMTNPSRWAAYSRQNLENILLAYTSHEIETLVKRLHTHMVNDFGYHQE NAINNVLCDKLWSCIQGQTVSLYLKLYTVIDKHYRGTNIRFTKNDIISAFEEYKNA P33332 Exocyst complex component SEC5 Saccharomyces cerevisia S288c S288c 0.112236875 1 LEVO MDRFQIGDEQLLRFYQLKTINPTHSWAQDSSKLNNEEATSNELGVETSFDILKDFKYGNQISIDKESRAYLNDESLSYIR DPLNGQEMSKELQHLPNDSMRLNYLVNSKQFNVKAFLRDMHKQDSFNDLNNSLDRLDSDIQDQSIHLKQLVGKNFTKYVK IKNKLDQIYKEFDEKTNEKNQCDSPKENQINVESLNKKVDEVIRTTTFKLKPLMDNYQKILNYQATKKFIELNKFYFNLP KSLKRCLTNNDFNEFIIEYSKGLTLRRRFNQSSDASQSLVIKRIWTQIENLLVTYKDLIWNSLINSNFNIDQPQETILSL FSKLLNLENFINNNQRESESGNKNTTSSSNENPILRWMSIKMNGFQNELNELSGHMISKIIHSQRLILQNNTNQDKSQGC VELSYYLKINQLFQIISDTGKDSEGLKSTVEPNKVNTISGTSYLNLNCQPSSQGLTDSPTIIEMWLLILKYINDLWKICD QFIEFWEHIEKFLDGTYQNSIINEKRKENILIGDSNIIESYQKSLILKEEQINEVRLKGEEFITSVSQNLISFFTSSQSS LPSSLKDSTGDITRSNKDSGSPLDYGFIPPNCNGLSCLRYLPKIVEPILKFSTELAQLNITTNGITICRNTLSTIINRCV GAISSTKLRDISNFYQLENWQVYETVTFSSKSQDSSKNLTFEYGVTQFPEIVTSFQEVSIKTTRDLLFAYEKLPIINGIS VVSYPSKQLLTGIEIQQIISMEAVLEAILKNAAKDKDNPRNSHTILTLTNLQYFRECAFPNILQYFDDAFEWNLASKNLE LFSLLSKMESSIFGNYLSDLKINLRDTLEEKFHEINWPMYTSNSFRVGDYIIEALMILIVVHSECFRIGPQLIHKILIET QIFIARYLFEAFKPYVGNLSNDGSLQIIVDLEFFQKVMGPLLEKDTEATLRACLQNCFQNDTNRLQKCINEINPIVSANL KRTAIQFAAFS P89102 Exocyst complex component SEC6 Saccharomyces cerevisia S288c S288c 0.09353970299999999 1 LEVO MSSDPLQQVCDLIKGDLSLERVRDIKEQLLKEKSVVEYQLNKESDKYYGEVEESLKLLNLSKNSVTSIKQQINEVNKLGN DNRFAINRYDILFRATKLYETVNTTSSIYDRIYNFVALMEHIERLLVAELAEDALETGCPHLLEIHFLLTSARDFQEQVV VMAKEATEDAQRTVMKLFSRLSGIISKFDKLLDGLTYDIVEMARAEQISLAIRLFKIYDLEEREDLRIEAIRNIIKKKEI EIEKSSIKKLPNSKNTARLQDETPKVIEYPTNKGLYQEIMSGTISTRTAPRGYKHFLINGINNSISEMFGEMREKYVGDQ KFDVLDNMDWIFNELIIVKEHIANCCPPHWNIFEVYFDQYYKELHSLITDLVESEPETIIILDILAFDKTFQDTLKQDFG FTKSEVKSVIGDKEKETLFKDYLNLIVVKMTEWIGNLEKAEFDVFLERSTPPHSDSDGLLFLDGTKTCFQMFTQQVEVAA GTNQAKILVGVVERFSDLLTKRQKNWISKISEEIKKQINYNHKYDIDPESITPEDECPGGLVEYLIAVSNDQMKAADYAV AISSKYGKLVSKVYEKQITNHLEGTLDGFAEVAQCSSLGLITLMFDDLRKPYQEIFSKTWYMGSQAQQIADTLDEYLLDI KPQMNSVLFVNFIDNVIGETIIKFLTALSFEHSFKNKNNKFLEAMKRDFEIFYQLFVKVLDGNESKDTLITQNFTVMEFF MDLSCEPIDSILDIWQKYLEVYWDSRIDLLVGILKCRKDVSSSERKKIVQQATEMLHEYRRNMEANGVDREPTLMRRFVL EFEKQ P32844 Exocyst complex component SEC8 Saccharomyces cerevisia S288c S288c 0.12236710899999999 1 LEVO MDYLKPAQKGRRRGLSINSLSETQQSAMNSSLDHLQNDLNRINLQWNRILSDNTNPLELALAFLDDTSVGLGHRYEEFNQ LKSQIGSHLQDVVNEHSQVFNTNVASYGKAVSSIMQAQEQTLNLKNCLKEANEKITTDKGSLQELNDNNLKYTKMIDVLV NIEELLQIPEKIEENIRKENFHQVQILLERGFILMNNKSLKTVEILKPINQQLELQEHLLFNNLIEEIHDIMYSKSNKTN FTRVTNNDIFKIISISHNGFTSLENYLYNIVNIDIMEHSKTINKNLEQFIHDQSLNKGNIMLQENAATQAPLAPSRNQEN EGFNRIGFLLKTINNINKLPVAFNIITERAKEEIHNIIVKSTESIRSKHPSLLKMATSLKNDNHFGLPVQDILSIILREC FWEIFLKLLYAIQCHRAIFEMSNILQPTSSAKPAFKFNKIWGKLLDEIELLLVRYINDPELISSNNGSIKPINGATNNAP TLPKRKNPKIFSLEYNIEDNSSVKDQAFELKALLKDIFPGFSVSSNMDLDSIYVKDESFEQDEPLVPPSVFNMKVILDPF LLFTQSTSTIVPSVLTQNTISSLTFFDDYMNKSFLPKIQMTMDYLFTVEVESNNPYALELSDENHNIFKTALDFQRLFYN LLNVFNTANTFREKISYCILDLLNHFYNYYLGLFNSLIGTSDRHLTRKIITAWLQNGILMDQEQKILNGDETLFHEESIE LFKEIPHFYQAGKGLSKSDLFNNLTLDTILQFSASVLWILNWLPGLKKAINIDEVSQEPMLDADRLRSSWTFSESMDLNY SNPSSSPNSLGNLKILLDDKASKKFDETIDGFKTLKFKLITILRFNIRALCIYDIGSFFQNTKIWNMDVGSIELDQNIAS LISELRRTESKLKQQLPEKEKNSIFIGLDIVNNYALIKGAKSIKVLNHNGIKKMLRNVNVLQHAYRNLSSEPSKINMNVT MNFYSLCGSSEAELFEYIKDNELPHCSVEDLKTILRLQFSEEMHRQLKRQSTSSTKGSIKPSNKRYTEALEKLSNLEKEQ SKEGARTKIGKLKSKLNAVHTANEK P32855 Exocyst complex component SEC10 Saccharomyces cerevisia S288c S288c 0.100459578 1 LEVO MNSLYELDPKWKKLLKTDNFLGGLTVNEFVQELSKDHRNDVLIDANTKNLPTNEKDQDAIREAIWKQLDPKPYIRTFEST LKELKNLNEETLNKRQYFSEQVATQEVIHSENVIKLSKDLHTTLLTFDKLDDRLTNVTQVVSPLGDKLETAIKKKQNYIQ SVELIRRYNDFYSMGKSDIVEQLRLSKNWKLNLKSVKLMKNLLILSSKLETSSIPKTINTKLVIEKYSEMMENELLENFN SAYRENNFTKLNEIAIILNNFNGGVNVIQSFINQHDYFIDTKQIDLENEFENVFIKNVKFKEQLIDFENHSVIIETSMQN LINDVETVIKNESKIVKRVFEEKATHVIQLFIQRVFAQKIEPRFEVLLRNSLSISNLAYVRILHGLFTLFGKFTKSLIDY FQLLEIDDSNQILSTTLEQCFADLFSHYLYDRSKYFGIEKRSLEAILVDMTSKFTVNYDKEINKRVLLDKYKEKLSTNVD AFMHSPRGNTHSRQDSTSRSKLSQFNSFLKTHLDKDHLSLNRTNTLSDSFNNSSSSTQYDVANNSSSLVNSSFTASDIDN SPNSPANYSLNDVDSMLKCVVESTARVMELIPNKAHLYILEILKIMFLGIVDSYMEIALEVAYWKICKVDINKTAGVVNL NFLKFISMSTEILDLLSISIKSIFLPLLNNSPEIKAQIIEMTNSQIQKMEILINIILQETITVISTKFSAILCKQKKKDF VPKSQELLDQDTLPAIEIVNILNLIFEQSSKFLKGKNLQTFLTLIGEELYGLLLSHYSHFQVNSIGGVVVTKDIIGYQTA IEDWGVASLIDKFATLRELANLFTVQPELLESLTKEGHLADIGRDIIQSYISNREDFNHDNFINSVKLNFR Q06245 Exocyst complex component SEC15 Saccharomyces cerevisia S288c S288c 0.105166641 1 LEVO MDQEGQPLLSKDFQQVLLATASGNNSSWTERAVLNNESTDAVKHEPALGQNDVFDLDPLSFDKWVPFLRRALDKNQLDPV IDELENSIEDNFQGLELQLLQDSQMNDKLETSIDEIANIQGMVQDTLSSEISKFQIRLSESANELIVKKQMYVNNKKISL KISEATILITKVVRILELSSKCQELITERKFFKVLQNLDSLEKLYLQEFKNYNFQFLIEIYNSIPFLQKVTKDECINLIR NSLNLNLGKNLIKVGQEFVAIYENELLPQWLETRSKMKLTNFKFNSPIEISMRDESFLAKLNLGEFFQLDDFHDSIMIFQ NLNELSVLSGEFNKEYELRKTKLMYPLIWKKNKTAAYQMDSLLRGTGTTPGSTAHDVSTDDPFTQSLSLHFLQDYFLKIL GFLLYDINLNKATEFILVDNNYNSTNEFWDGLMDRLSPYLSYFIDEKLKTEEDMIKLKDFLCIYVAILENFKLNIEPLYK ILVSIFEKFCSVSLRAFDDEFQILLNDDDFMPLSINDKTLYEKVLKICWMKEGEHLSLPDPTNGEPFAVTLPFSPLYPMT CTLAKKTYSKITAFLSIFYRHELHTLNNILVKTMDDIFNDIVNKKIRSKLESTSREEIAQILVNLDYFIIAAKEFSNFMT RENILQNPDMEIRLSSIKYLAESRKLAETKLIELIDSKISDILETIEIDWQITEVRQDPDISIIDLAQFLEMMFASTLQN LPYSVQTLLIFREFDSLTRQFMGLLLHDTPSTITHESIMNFEVDVNYLESIIPRIFPSTPGTIDSNGYQSPMTPSTPTFP NANGVDAPTLFENNIKSLEATFMELKQCIELLKTQGKDYNEPEIRLRKYSRIRQEDAALLLSKIQHFVSSVEGANGDDTS VMDSSSIFNSESASVIDSNTSRIAKFFNRR P22224 Exocyst complex component EXO70 Saccharomyces cerevisia S288c S288c 0.071382328 1 LEVO MPAEIDIDEADVLVLSQELQKTSKLTFEINKSLKKIAATSNQSSQLFTPILARNNVLTTLQRNIESTLNSVASVKDLANE ASKYEIILQKGINQVGLKQYTQVVHKLDDMLEDIQSGQANREENSEFHGILTHLEQLIKRSEAQLRVYFISILNSIKPFD PQINITKKMPFPYYEDQQLGALSWILDYFHGNSEGSIIQDILVGERSKLILKCMAFLEPFAKEISTAKNAPYEKGSSGMN SYTEALLGFIANEKSLVDDLYSQYTESKPHVLSQILSPLISAYAKLFGANLKIVRSNLENFGFFSFELVESINDVKKSLR GKELQNYNLLQDCTQEVRQVTQSLFRDAIDRIIKKANSISTIPSNNGVTEATVDTMSRLRKFSEYKNGCLGAMDNITREN WLPSNYKEKEYTLQNEALNWEDHNVLLSCFISDCIDTLAVNLERKAQIALMPNQEPDVANPNSSKNKHKQRIGFFILMNL TLVEQIVEKSELNLMLAGEGHSRLERLKKRYISYMVSDWRDLTANLMDSVFIDSSGKKSKDKEQIKEKFRKFNEGFEDLV SKTKQYKLSDPSLKVTLKSEIISLVMPMYERFYSRYKDSFKNPRKHIKYTPDELTTVLNQLVR P19658 Exocyst complex component EXO84 Saccharomyces cerevisiae S288c S288c 0.085649672 1 LEVO MVEFSLKKARNNWKHVKKSASSPAKQKTPPSPAKPKQKTKKNPYSDLKDPATSYTLPTINARERSRVATSMQRRLSIHNT NYAPPTLDYSMPLPDMPNMIVPNDNVDSSHNNSSFTTENESVSSKGPSNSLNLSTADLSLNDSSYNKVPARSAMRNTVNP SGSNDPFNNSTSLRKMLANPHFNAKDFVHDKLGNASAITIDKFTSNLTDLSIQVQEEVKLNINKSYNEIMTVNNDLNVAM LELKRVRANINDLNEVLDQCTKIAEKRLQLQDQIDQERQGNFNNVESHSNSPALLPPLKAGQNGNLMRRDRSSVLILEKF WDTELDQLFKNVEGAQKFINSTKGRHILMNSANWMELNTTTGKPLQMVQIFILNDLVLIADKSRDKQNDFIVSQCYPLKD VTVTQEEFSTKRLLFKFSNSNSSLYECRDADECSRLLDVIRKAKDDLCDIFHVEEENSKRIRESFRYLQSTQQTPGRENN RSPNKNKRRSMGGSITPGRNVTGAMDQYLLQNLTLSMHSRPRSRDMSSTAQRLKFLDEGVEEIDIELARLRFESAVETLL DIESQLEDLSERISDEELMLLNLISLKIEQRREAISSKLSQSILSSNEIVHLKSGTENMIKLGLPEQALDLFLQNRSNFI QDLILQIGSVDNPTNYLTQLAVIRFQTIKKTVEDFQDIFKELGAKISSILVDWCSDEVDNHFKLIDKQLLNDEMLSPGSI KSSRKQIDGLKAVGLDFVYKLDEFIKKNSDKIR P38261 singleParticle particle 0.3 7.4 150.0 NaCl sodium chloride 10.0 C8H18N204S HEPES 2.0 DTT

Solutions were freshly prepared from stock and filtered with 0.22um membrane to avoid microbial contamination.

Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE 60 AIR

Purchased Quantifoil R1.2/1.3 gold grid was directly glow discharged 60 seconds before use. Before glow discharge, the sample chamber was vacuumed by an air bump for 2 minutes.

ETHANE 100 301 FEI VITROBOT MARK IV

Protein sample was applied onto a Quantifoil R1.2/1.3 golden grid and hold for 60 seconds, then blot for 2.5 seconds before plunging..

This sample was mono-disperse.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 2.0 1.8 3.0 3.2 22500.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 113.0 123.0 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3838 3710 0-31 11 6466 8.0 50.0 1

The selected image stacks were motion corrected by Motioncor2 software and distortion magnification corrected by script.

904481

Semi-auto-picked by RELION1.4.

30 50

4516 tilt-pair particles were picked by EMAN2 subroutine e2RCTboxer.py in an interactive RCT-boxing mode. A low-resolution 3D map was generated by SPIDER.

1 C1 FOURIER SPACE 4.4 FSC 0.143 CUT-OFF RELION 1.4 343342 ANGULAR RECONSTITUTION RELION 1.4 ANGULAR RECONSTITUTION RELION 1.4 4 100000.0 RELION 1.4 2B1E A 67-623 PDB experimental model RIGID BODY FIT

Exo70 (a.a.67-623) was first fit into the map with Situs as a rigid body. Then it was split as Exo70 (a.a.67-344) and Exo70 (a.a.345-623), and fit into the same position with Chimera.

REAL 2D2S A 525-753 PDB experimental model RIGID BODY FIT

Well fit by one step Situs fitting.

REAL 2FJI A 411-805 PDB experimental model RIGID BODY FIT

The fitting position of this chain was determined by cross-link mass spectrum.

REAL 5H11 A 195-708 PDB experimental model RIGID BODY FIT

The yeast Sec10 (a.a.234-867) model was first obtained with Swiss-Model prediction based on this zebrafish originated initial model, and then fit into the map. Local adjustment was made with Coot. Final refinement was proceeded with Phenix real-space refinement.

REAL 1ZC4 B 171-283 PDB experimental model RIGID BODY FIT

The yeast Exo84 (a.a.346-470) model was first obtained with PHYRE2 prediction based on this rat originated initial model, and then fit into the map. Final refinement was proceeded with Phenix real-space refinement.

REAL 2A2F X 383-699 PDB experimental model RIGID BODY FIT

The yeast Sec15 (a.a.482-896) model was first obtained with PHYRE2 prediction based on this Drosophila originated initial model, and then fit into the map. Local adjustment was made with Coot. Final refinement was proceeded with Phenix real-space refinement.

REAL BACKBONE TRACE

All remaining models were manually built as backbone tracing Poly-Alanine, yet the present residues are shown as original. The backbone trace was guided by the EM map connectivity, secondary structure prediction and cross-link mass spectrum. The model was validated with different sets of cross-link mass spectrum data to confirmed the correctness.

REAL emd_6827_msk_1.map emd_6827_msk_2.map emd_6827_msk_3.map emd_6827_msk_4.map emd_6827_msk_5.map emd_6827_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 470.3544 470.3544 470.3544 90.0 90.0 90.0 X Y Z -0.05161394 0.109504156 0.00027629908 0.002879865 1.30654 1.30654 1.30654 AUTHOR ::::EMDATABANK.org::::EMD-6827:::: Cryo-EM map of the yeast Exocyst complex head-part structure at 6.7A resolution emd_6827_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 470.3544 470.3544 470.3544 90.0 90.0 90.0 X Y Z -0.03339365 0.11969313 0.00027287958 0.0027617707 1.30654 1.30654 1.30654 AUTHOR ::::EMDATABANK.org::::EMD-6827:::: Cryo-EM map of the yeast Exocyst complex top head-part structure at 6.2A resolution emd_6827_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 470.3544 470.3544 470.3544 90.0 90.0 90.0 X Y Z -0.04308945 0.13705194 0.00023243942 0.0024534639 1.30654 1.30654 1.30654 AUTHOR ::::EMDATABANK.org::::EMD-6827:::: Cryo-EM map of the yeast Exocyst complex bottom leg-part structure at 4.6A resolution emd_6827_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 470.3544 470.3544 470.3544 90.0 90.0 90.0 X Y Z -0.2781486 0.39413112 0.0002965994 0.0061325063 1.30654 1.30654 1.30654 AUTHOR ::::EMDATABANK.org::::EMD-6827:::: Cryo-EM map of the yeast Exocyst complex body-part structure at 4.4A resolution