2026-09-23 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-09-03 2026-09-23 2026-09-23 2026-09-23 Danish Council for Independent Research 0106-00010A Denmark Chan Zuckerberg Initiative 2021-234620 United States Jensen RK Xue L Mahamid J in-cell cryo-ET, Protein Folding, cell surface, Translocation, Sec-machinery, TRANSLOCASE Jensen RK Xue L Marotta F Somody JC Selkrig J Lenz S Rappsilber J Savitski MM Kosinski J Typas A Zimmermann-Kogadeeva M Bork P Mahamid J To Be Published 0353 9slc FULLOVERLAP EMDB EMD-54986 associated EM volume

Closed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells

Closed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells Closed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells 0 1 2 4 5 6 7 8 9 Mycoplasmoides pneumoniae M129 29342 Protein translocase subunit SecA Mycoplasmoides pneumoniae M129 0.091942234 1 LEVO MGLFNFLKLVSPRHRIYHKASKIANEVEGHKNYYRNLTDVQLLEESNKLVDLVTKQNYTILDVAVAALALIREVVYRETG EFAYRVQIIGAYIVLIGDFAEMMTGEGKTLTIVLAAYVSALEKRGVHVVTVNEYLAQRDATNATKILKRVGMTVGCNFAN LAPHLKQAAFACDVTYTTNSELGFDYLRDNMVHRFEDKKIRELHFAIVDEGDSVLIDEARTPLIISGPAKNEFAAYVAVD RFVKKLKEDEYKIDPESRAPALTELGIKHAEKNFKTDNLFALENSDLFHKIINALTAVKVFEQGKEYIVRDGKVLIVDHF TGRILEGRSYSNGLHQAVQAKEMVEIEPENVIVATITYQSFFRLYNRLSAVSGTAFTESEEFLKIYNMVVVPVPTNRPNI RKDRADSVFGTPNIKWLAVVKEVKRIHETGRPILIGTANIDDSELLHNYLQEANIPHEVLNAKNHSREAEIVAKAGQKGA VTISTNMAGRGTDIRLGEGVAEMGGLYVLGTERNESRRIDNQLRGRAGRQGDRGETKFFISLGDALFKRFAHDRIERAIT KLGNDTFDSSFFSKMLSRTQKRVEAINFDTRKNLIDYDHVLASQRELIYKQRDKFLLATDLSDMIDKMLEKFVEQFCDQY RNPKNQNLVNHIALSEALNLELNMHGVISPKLFENMTFDATVHKTHSLIGEKITNKVKVLTPPIALIRFREIMITAMDKH WIEHLDNVFKLREGVTLRSMEQTSPLNVYIRETDILFQTMLQKIARDVIIQIANLATPEEFDEELMKANALKKLQALREA HEKSNEGQ P75559 7.4.2.8 Uncharacterized lipoprotein MG307 homolog Mycoplasmoides pneumoniae M129 0.13621667199999998 1 LEVO CATPSNSALQTVFKARSSQFFNGEQGSLQSALTTALKNPVANKQFIAAPLLKALEAWYENNEDKKITQFLKDTKSNVDSQ YTTAVDKVVSASRNKSLFVQQDLLDNAGGSEATWKAQKLLEQLISDFASRVFQKNYLNYKKDGQVSTGPFTYDELHKEES WKNFEFSAPRFSETNDDFFAKIQSQVFDQWVEYTDPTLISQVNYKYSAPSQGLGQIYNREKLKDKLTPSYAFPFFAEEKD IAPNQNVGNKRWKQLVKGEGAITDNNIGQSGTNSQKTGLLKYRNESNKGDFLDFPLNLSDTNETKQLVDASNIVDQLEAA NLGAALNLKLQVFEQDNDELPQIKELKEDLNNTIVVDKSKDVEKASKTNALFYNDQEGKQQQSDSDPIAGALDDIFAQNT SEGTNLSKLAEQVKKAAATKMEAKTAVLRTNNSKGQQNNYVVLDAAIPTFNSTTSKSKNNSASNEVLVALKSGSINLRQV QQTDQNSYSPIKFRIVRNSTGVTVFGLDGGSYYLKQDSTNKKSVSKQSLTLLTKSSSGNSNKVLRDLDKQKQFLKFRAFQ AKTNTFYSTNFAFSFPLNETLKSWFDKHRELILANALVNASLDQKDKASKALTEAFNPYKELIKEFAPVALATTMISFYF DQMKALNNKLLERARNLNQNVNQANPTPWLNGLSAKLPYVNTNGNYEKLNNYFTFLITKTLWPKVGQEETSISEESNKLK TKTADVDKIRDKILENIQTKVNDFVKNKLKPALAPRPAYSNVILLNVNNDKVLSSGANWSLASLLQSDKVNPLSFMLLKQ AFDNNDLFKKAQKLFKDIQEKSSNNGGMQSSSTTNSDADALSKVIGNYYYTTWAKLTDKSIYGNPKDNKFDELFKLAFEA SIDEKSFNVDYKAVIDHYRFIYTLQWLVDQKLKNFKSLLKTNLKFGEVAFIAYKNTETTNFSNPQGVFGSYFNYENSASE VKESTQTLDPNNFFYKTTTKPTVQAIQQVASLALVQKQQMQQNSTDHYGFTGLSTSTSSMFDASSRDAILQQITKTSLQQ YGSKDQLKKIIQGTNNQLLLDRIAVQLSGLNPSTTNGGSGKTIATYFQVDAVGNPTLDFQAKRKLLLDLLDQYQNYFGNG AQKSQRDSTPSGTGNYLTYQNGSDKYTYTQFTYQDIDSLSLTTTSGTNNKIASDVVAALLLFQAADKGTQQLALSAINKP QLNIGDKRIESGLKLLK P75342 Uncharacterized lipoprotein MG309 homolog Mycoplasmoides pneumoniae M129 0.143385078 1 LEVO CAQPTASTVEGLFKPSSAFADRTDFSLSSILQKSLINRESFNQYLAMRLAPVLRTFYEDNYDTDIKERLNGFTADTDNAF VSQEQNLRNQFRENYLVHLQTDIFDNTGGNQAAWKLRDVNNKIIDDFISRIFAKNFVEYVQDGVGPLTKPTKSLIENTSN FKNIKLQPKFVNKNAKLKINNDAVYAAIQDKLLDQFITNENPNLVSRVVFTNETPVDGFDNYFNTKVIQSPTPSYQFQVF NKYNQQSGGTKGANGFNLLASNLKSYKNDQSKGIDIPNKFSSDSGGKLLLKASDMFDTFDPSFSAAFIQGYLALQKKSKG ADSKEVDSLIKDKSIIENFFVDNNTQAAAAARAASSSSEGTIQLKTASDGGGTTQSTVHKTDLVKIFGDKDVFAGEYKQQ IGNTNANQTGGGGSGGGGGTSTGSSTGSSTETTTGNSSKAVVDLIEVKKDSSSQPDYILSRGKDGIHLMAVDGGSHYLTE SGRDVAKQKKFLLFRALQTKYGLVDTDTTYDFKLFDEVKKYFDTNRILFLFEALLDLSSDTNNKDNFLSYPQFKKFADSI KSIEKDLKELVQAHYKQAVFNETAVAENKVTLKLAERNQPFIDNERNNQIEQNGLAAKLPYEQDAKTGHYNDLGNYYKDI IDNVDKKGTSTVKTTSSNTGQTKNFSEEVVSKLKDNKKKVEEAAKKHVEALKVFTIPSPLYSQVILVQTKLSFTPESTSL GLNLALNNYLTSTELQNSIKLSYFQEDEAFKKIIDITNLTFSQQSGGTGGTNGNNNLTADNWKIFKETYLLDLFESQAQK SIFGHVGSSDKNSSTKTGIEGVLDTLYSSLNLEERLDSDDVIDYLSYLYTAHWLLKDNLKNYKQSLQSKLSRTSNAFLVW SVDSEKNKNDSQSTLSSTASSTSNTGLIQLRSVVSLAQNQAAGQGGDNNSDITQTEVKNPNFVFGSSVYDWTNSKTPEVN RAADDTSSFFYTKSSSSSTGAAQSSATVLRSLNQASGMTTKTAKNRYGFRGIVTSSTSGSLPEAVSRRLFKQFVNQTEKG VKVGGQMLITTAKSGKATLVLKQQADDAESTTNNAYKGALFSFGSMDNLKNIINGIQTQTEFDALYNHLTSDLNIDVTGV DKNKTLTEQKTSLTSFVDSNFKQSTQSAQRGDTSARSARSATVQIKKTQEDNQNTNYKDVFSRFDGYIGDNKVEEKNYTS YQFLSDGGKYHATFVKQVNLDDVEKIGTDSLKQEDSSKDKRLNLSLEEFLAAIALEALDPNNQTQAINALISGNKKGLVK VGDFRIFSSISAQWVRRF P75334 SecDF Mycoplasmoides pneumoniae M129 0.108345633 1 LEVO MGLKKRVSFDWLLKIGIILVLAFLGLFGIIFGSYKLLNDSRLGVVFNGSTTTTVYFLNHKSKDANKELDPTQKKDGNGSG NNTEMITDVNGFLNNIEKSYANSLYAQGFSSVNITKNSHDTSAKELSDKGVFDSSWLVNDGLPSISVTFEQRREEARTRA RKRQIDAQVKRNALSAIEHNYKLSLETTDGIVLFDSFDKEFIRNSLTAVVPQTTNTNSALTFEYKLSKNVITKESLHNDF LDFIKSKSLTDSDYNTGNGQKSVEGSGKWFKDKANGSAQNGNKTLVLWKDKEGAVQYVRNIFNVPKGGTDYLTFNEREKN LWDFLHAEGNFSSGDNLFLQKNNNGNSPITKASDITLKNIYYIYAAPTHFSQVATKDNNNKDAADVVAVANSADTRKLRS GDATGFSGLFSNYILAEIRTEDPVAKNGDPVKVNATLQSFLDSNNQRLEHGGNIKFQVANFVNNDGSYVPASYLEASRVK VLLSNGFPETATIAAANTKLVNAPLSNTLARDVSNFASSFIALGVIILLATIALGIRYKLLGLYKALALALSAISSLAFF SAVGGVVDVFSFVGIFFVVAVNIINLITLAELFLRNIKNNASIVESWKLCLKRSFFTMIETHICWLLSALVVIYLSNYQV QQLGTLMAVSAITSYFLNYGLGVILVWLFVSSHSGLEWRFFLYKKDAQALTKTSSNYSILTENNDIQTDFFISKNQHDFF GKKKWSLLFIWLTVLAFGVVMLGLYLGAPQLLGNFLAADIESSTGIMLGVGVISLLYLLYSLPRYGVAYGISYLIALILL AAGLFGAMYLANFIFRIDQSTIQLIIFVYLFWLFFQARIGQTTIWTYCYWFKRSLKDRVFVKNLFNDNVNSQWRLDLIGS SVLILLFIVYAAFNFGGINGTINLVIFYLIAIVALFSVFVNGLPLFSFGLINGWLSPYNYVQIHITLRHKKQMFKEVDQI EEQLISGINSF P75387 SecE Mycoplasmoides pneumoniae M129 0.014489403999999999 1 LEVO MEKKKLPFGLKNKEKLTAYNDEKIHELHRQLKAKIEAKKAKEKQDSKTKDTDKKVDQTPKVKVPFTKKFSNLWFGIDKEV NKIVWVTSKKLITIFLLIVLVSAIMIGIYFGINHLFIALGVFKGK P75048 Uncharacterized lipoprotein MG338 homolog Mycoplasmoides pneumoniae M129 0.140427859 1 LEVO CSALNTSNLFPRQNRSKQLIGFTENNIIKPEAVLKAALAEDNGTETILRVNFGEALKSWYQNNKDRNIATRLTIFSENVE DEHDNLLDQKQQAEPINWPIELQKEYDQWGGSESSWKALKLYDRLIADFQSLIFSNIVANVQLTDGSDQFKPTTKDNLDS TSNKIKFVNSKPNDPNGEFFANLQAYLFAQWVVEENPLPLTQAFFAYQAPKDGLDSLYDQAAIGSALQLGYAFPAFREPN NGQSQGKTTFDPTPNSAQNFGDFIKAVFPEQKNGQTQQSNTSSRTGLFDWQTKWNTNGAANKLLVTKSNLRGAFKGVGLA TAIIDQYEYLVGGSKTSSLPEVKVDSNKSNQNPLDSFFMEGKDAVAIRSIVSRAKIAMTDQTPGFKVNPAFVKVKQSQQN DTFYQNQRKLSGGQSGDNNSQGKHHYLQDAVRLTSSQAMAAASTGADSSSGTNVGGSSGGNSVLIPLPRSAALTHTQQQV QQTTSTLQTPVYARGDDGTYALAIDGGDYFLANNKRDFTKQADILLYRYLQAKSNNFKENGVEFSLNLLESGSLFQTWAQ TGLTAKLYGALVAMMGSGQGTQVKGSVQGSSRAASVSVQTTQQNRQQSTDTQESEVVKLAKSLLKSSADLAKPFTDNPTF KKALTDIQSEYKDYLAAAGKLSEFKKDLGEVSGLQQAIIDRADKYIQLEKQAQKSAIGLGQPLPYQRASDGSYPALEKFF IPEDSAADGKVKASESGSAALVTLKTTDSQKSTNTVKQPDIKPTRENNDKKLKQLTSDVETKASSLITKWGATPQIGSQF SEIVSLKSKDNKPQTNMILALLSDVGIKWTKILNSFKEWFFTNTNDFKNNYDSEKKELKGNEYKDFNDLVKQTLYLRSWQ RLTSKEKFGYYKELGSVKAQAAQSGMVSLSSSAAVANAVASSGMQKSGDQTLLELGKKAFESELEASSSDGQYKYLRFLS TLMWLVKDGAKNYKRLLQQAITVGTRAFVSWTVSYDDTATASAAAAKAQVAVLKTAQATNTQSDNPFNKFVQNPDYVQGS ETNWFNDKSTPIKPDSLLESESTYNFTAEPFDDKTKSQKRSTGGTTNEKHFFGFNGLTINSPQSVSTASAGLTEQIFNNF GQLVTSSDKSGALSQYKDKATLKRLIQNTNSDAELNAFGEVLHRAVNVDTSNLGRFNSSGEPLISFDNKKKFLVDVVDKL DDVYFNKFEGYVGQTKVKMSDSSSSSQGTKTIRKPKPHHSPRTRVSRLWAMSFRLPTRTLTKFLLVEKLIRTVL P75296 Probable protein-export membrane protein SecG Mycoplasmoides pneumoniae M129 0.008352255 1 LEVO MDAIQIVMFVMAILCLIIGLLLSNHGSTGGLASLSGQDLEIFRKTKDRGIVKILQITMFILVVLFLILGLVFHFAL Q9EXD0 Uncharacterized lipoprotein MG348 homolog Mycoplasmoides pneumoniae M129 0.030410285 2 LEVO CSNIDKPNVFRTLSQQSVENKVDYSKLPKENKTVRNLVFGTAEYNDGNYVLVVTTETDSSQINFLNGSNNQAVSTENWAG DLGTTVKQVQNRYSTYPKGVKFLIWNDIDPNPVKWNPFARYPVIASDNELAKQTDKDNSDKLRRNDESAIQYREIVTFIQ TVYSGSVNNLINQSNVHAQTVGTDVTKAIVIAFRKNNLDQISAHFYNPDNSNGSNAPGSNQPNQDSGNNGSTTPAAPAAA AAKKSYSAGSFGVKRHAVQVSINFLNFLDSVYTPLN P75255 Protein translocase subunit SecY Mycoplasmoides pneumoniae M129 0.04896529299999999 1 LEVO MQAKPTTAVKQKQNFGQRLFTLLRNRDFMISFLITVVLLVLFRVLAIIPLPGIQVNQTGLDQNSNDFFSLFNLLGGGGLN QLSLFAVGISPYISAQIVMQLLSTDLIPPLSKLVNSGEVGRRKIEMITRIITLPFALVQSFAVIQIATNSGGGSSPITLK NNGSDFVAFYIIAMTAGTYLSVFLGDTISKKGIGNGITLLILSGILAQLPEGFIAAYSVLSGVVVTINATLTTAISFFIY FMAFVTLLFATTFITQETRKIPIQQSGQGLVTESSALPYLPIKVNSAGVIPVIFASSIMSIPVTIAQFQPQTESRWFVED YLSLSKPTGIVLYGILVILFSFFYSYIQINPERLAKNFEKSGRFIPGIRPGKDTEKHIARVLVRINFIGAPFLTVIAIIP YIVSALIHLPNSLSLGGTGIIIIVTAVVEFMSALRSAATATNYQQLRRNL Q59548 subtomogramAveraging cell 7.4 ETHANE-PROPANE HOMEMADE PLUNGER

Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental chamber..

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.5 3.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 2.9 1 2 C1 9.1 FSC 0.143 CUT-OFF Warp 2.0.0 11557 355 13770 Data-driven, Iteratively improved Manual picking and Deep-learning based particle picking Warp 2.0.0

Initial particles were manually picked and used to generate training data for iterative rounds of DeePiCt particle picking and junk cleaning with 3D classification in RELION. A final round of multi-class particle picking was performed in DeepFinder followed by manual curation of the final particle positions. Subtomograms were extracted in Warp.

Warp 2.0.0 PHASE FLIPPING AND AMPLITUDE CORRECTION 5 209.0 RELION 4.0.1 RELION 3D classificaiton

Classification divided into two main classes, one corresponding to this class, and another similar class but including substrate in the dome cavity

MAXIMUM LIKELIHOOD Warp 2.0.0 AlphaFold in silico model RIGID BODY FIT

Fitting was performed using PowerFit and Fit-in-map in ChimeraX

REAL emd_54986_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 294 294 294 0 0 0 294 294 294 499.947 499.947 499.947 90.0 90.0 90.0 X Y Z -0.0058762454 0.015533497 0.00006160008 0.00052539795 1.7005 1.7005 1.7005 AUTHOR ::::EMDATABANK.org::::EMD-54986:::: Closed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells. Denoised (M) emd_54986_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 294 294 294 0 0 0 294 294 294 499.947 499.947 499.947 90.0 90.0 90.0 X Y Z -0.017853389 0.029462494 0.000059595808 0.00079697376 1.7005 1.7005 1.7005 AUTHOR ::::EMDATABANK.org::::EMD-54986:::: Closed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells. Sharpened (M) emd_54986_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 294 294 294 0 0 0 294 294 294 499.947 499.947 499.947 90.0 90.0 90.0 X Y Z -0.007135141 0.015295892 0.000059595808 0.0005695235 1.7005 1.7005 1.7005 AUTHOR ::::EMDATABANK.org::::EMD-54986:::: Closed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells. Unsharpened (M) emd_54986_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 294 294 294 0 0 0 294 294 294 499.947 499.947 499.947 90.0 90.0 90.0 X Y Z -0.0964647 0.10320788 0.00006039286 0.011810569 1.7005 1.7005 1.7005 AUTHOR ::::EMDATABANK.org::::EMD-54986:::: emd_54986_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 294 294 294 0 0 0 294 294 294 499.947 499.947 499.947 90.0 90.0 90.0 X Y Z -0.09356738 0.09725524 0.000058798756 0.0118826125 1.7005 1.7005 1.7005 AUTHOR ::::EMDATABANK.org::::EMD-54986::::