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 9slf FULLOVERLAP EMDB EMD-54988 associated EM volume

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

Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells 0 1 2 3 4 5 6 7 Mycoplasmoides pneumoniae M129 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 Probable protein-export membrane protein SecG Mycoplasmoides pneumoniae M129 0.008352255 1 LEVO MDAIQIVMFVMAILCLIIGLLLSNHGSTGGLASLSGQDLEIFRKTKDRGIVKILQITMFILVVLFLILGLVFHFAL Q9EXD0 Protein translocase subunit SecY Mycoplasmoides pneumoniae M129 0.052003633 1 LEVO MQAKPTTAVKQKQNFGQRLFTLLRNRDFMISFLITVVLLVLFRVLAIIPLPGIQVNQTGLDQNSNDFFSLFNLLGGGGLN QLSLFAVGISPYISAQIVMQLLSTDLIPPLSKLVNSGEVGRRKIEMITRIITLPFALVQSFAVIQIATNSGGGSSPITLK NNGSDFVAFYIIAMTAGTYLSVFLGDTISKKGIGNGITLLILSGILAQLPEGFIAAYSVLSGVVVTINATLTTAISFFIY FMAFVTLLFATTFITQETRKIPIQQSGQGLVTESSALPYLPIKVNSAGVIPVIFASSIMSIPVTIAQFQPQTESRWFVED YLSLSKPTGIVLYGILVILFSFFYSYIQINPERLAKNFEKSGRFIPGIRPGKDTEKHIARVLVRINFIGAPFLTVIAIIP YIVSALIHLPNSLSLGGTGIIIIVTAVVEFMSALRSAATATNYQQLRRNLAIEVQKTAQQDKEEQLRAETPGIGNLW Q59548 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 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 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 subtomogramAveraging cell 7.5 Quantifoil R2/1 GOLD 200 GLOW DISCHARGE ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 3.5 GATAN K2 SUMMIT (4k x 4k) COUNTING 2.9 1 C1 17.0 FSC 0.143 CUT-OFF RELION 4.0.1 1001 183 6103 Data-driven, Iteratively improved Manual picking and Deep-learning based particle picking Warp 1.0.9

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.

Warp 1.0.9 PHASE FLIPPING AND AMPLITUDE CORRECTION 5 1500.0

Classification divided into two main classes, one corresponding to the open conformation (This class) and the other corresponding to the closed conformation.

MAXIMUM LIKELIHOOD RELION 4.0.1 AlphaFold in silico model RIGID BODY FIT

Initial fitting with PowerFit into the map of the closed conformation of the complex (EMD-54986). The closed conformation (PDB: 9SLC) was rigid body fitted into the open conformation of the map, and the AlphaFold3 multimer prediction of subcomplex SecYEG-DF was aligned to and replaced the old AlphaFold2 models of these proteins. The SecYEG-DF subcomplex as well as the remaining proteins were each rigid body fitted as single rigid bodies using ChimeraX fit-to-map.

emd_54988_msk_1.map emd_54988_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 56 56 56 0 0 0 56 56 56 297.69598 297.69598 297.69598 90.0 90.0 90.0 X Y Z -0.7863523 1.67954 0.0315954 0.27765706 5.3159995 5.3159995 5.3159995 AUTHOR ::::EMDATABANK.org::::EMD-54988:::: emd_54988_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 56 56 56 0 0 0 56 56 56 297.69598 297.69598 297.69598 90.0 90.0 90.0 X Y Z -1.6480972 2.3523316 0.030884096 0.3471655 5.3159995 5.3159995 5.3159995 AUTHOR ::::EMDATABANK.org::::EMD-54988:::: emd_54988_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 56 56 56 0 0 0 56 56 56 297.69598 297.69598 297.69598 90.0 90.0 90.0 X Y Z -1.5763819 2.4043565 0.032060035 0.3512007 5.3159995 5.3159995 5.3159995 AUTHOR ::::EMDATABANK.org::::EMD-54988::::