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- EMDB-54988: Open conformation dome complex including the Sec-translocon (SecY... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54988
TitleOpen conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
Map data
Sample
  • Cell: Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
    • Protein or peptide: SecDF
    • Protein or peptide: SecE
    • Protein or peptide: Probable protein-export membrane protein SecG
    • Protein or peptide: Protein translocase subunit SecY
    • Protein or peptide: Uncharacterized lipoprotein MG309 homolog
    • Protein or peptide: Uncharacterized lipoprotein MG338 homolog
    • Protein or peptide: Uncharacterized lipoprotein MG307 homolog
Keywordsin-cell cryo-ET / Protein Folding / cell surface / Translocation / Sec-machinery / TRANSLOCASE
Function / homology
Function and homology information


intracellular protein transmembrane transport / protein transport by the Sec complex / protein-transporting ATPase activity / protein secretion / transmembrane protein transporter activity / protein targeting / membrane / plasma membrane
Similarity search - Function
Protein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / Protein translocase subunit SecY / Protein secY signature 1. / Protein secY signature 2. / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site ...Protein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / Protein translocase subunit SecY / Protein secY signature 1. / Protein secY signature 2. / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Uncharacterized protein MG055 homolog / Uncharacterized lipoprotein MG338 homolog / Uncharacterized lipoprotein MG309 homolog / Uncharacterized lipoprotein MG307 homolog / Uncharacterized protein MG277 homolog / Protein translocase subunit SecY / Probable protein-export membrane protein SecG
Similarity search - Component
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 17.0 Å
AuthorsJensen RK / Xue L / Mahamid J
Funding support Denmark, United States, 2 items
OrganizationGrant numberCountry
Danish Council for Independent Research0106-00010A Denmark
Chan Zuckerberg Initiative2021-234620 United States
CitationJournal: To Be Published
Title: In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex
Authors: 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
History
DepositionSep 3, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54988.png

Downloads & links

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Map

FileDownload / File: emd_54988.map.gz / Format: CCP4 / Size: 686.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.32 Å/pix.
x 56 pix.
= 297.696 Å		5.32 Å/pix.
x 56 pix.
= 297.696 Å		5.32 Å/pix.
x 56 pix.
= 297.696 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.316 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.354
Minimum - Maximum-0.86619234 - 1.837118
Average (Standard dev.)0.031472065 (±0.28955787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions565656
Spacing565656
CellA=B=C: 297.69598 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54988_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_54988_additional_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54988_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54988_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Open conformation dome complex including the Sec-translocon (SecY...

EntireName: Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
Components
  • Cell: Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
    • Protein or peptide: SecDF
    • Protein or peptide: SecE
    • Protein or peptide: Probable protein-export membrane protein SecG
    • Protein or peptide: Protein translocase subunit SecY
    • Protein or peptide: Uncharacterized lipoprotein MG309 homolog
    • Protein or peptide: Uncharacterized lipoprotein MG338 homolog
    • Protein or peptide: Uncharacterized lipoprotein MG307 homolog

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Supramolecule #1: Open conformation dome complex including the Sec-translocon (SecY...

SupramoleculeName: Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

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Macromolecule #1: SecDF

MacromoleculeName: SecDF / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 108.345633 KDa
SequenceString: MGLKKRVSFD WLLKIGIILV LAFLGLFGII FGSYKLLNDS RLGVVFNGST TTTVYFLNHK SKDANKELDP TQKKDGNGSG NNTEMITDV NGFLNNIEKS YANSLYAQGF SSVNITKNSH DTSAKELSDK GVFDSSWLVN DGLPSISVTF EQRREEARTR A RKRQIDAQ ...String:
MGLKKRVSFD WLLKIGIILV LAFLGLFGII FGSYKLLNDS RLGVVFNGST TTTVYFLNHK SKDANKELDP TQKKDGNGSG NNTEMITDV NGFLNNIEKS YANSLYAQGF SSVNITKNSH DTSAKELSDK GVFDSSWLVN DGLPSISVTF EQRREEARTR A RKRQIDAQ VKRNALSAIE HNYKLSLETT DGIVLFDSFD KEFIRNSLTA VVPQTTNTNS ALTFEYKLSK NVITKESLHN DF LDFIKSK SLTDSDYNTG NGQKSVEGSG KWFKDKANGS AQNGNKTLVL WKDKEGAVQY VRNIFNVPKG GTDYLTFNER EKN LWDFLH AEGNFSSGDN LFLQKNNNGN SPITKASDIT LKNIYYIYAA PTHFSQVATK DNNNKDAADV VAVANSADTR KLRS GDATG FSGLFSNYIL AEIRTEDPVA KNGDPVKVNA TLQSFLDSNN QRLEHGGNIK FQVANFVNND GSYVPASYLE ASRVK VLLS NGFPETATIA AANTKLVNAP LSNTLARDVS NFASSFIALG VIILLATIAL GIRYKLLGLY KALALALSAI SSLAFF SAV GGVVDVFSFV GIFFVVAVNI INLITLAELF LRNIKNNASI VESWKLCLKR SFFTMIETHI CWLLSALVVI YLSNYQV QQ LGTLMAVSAI TSYFLNYGLG VILVWLFVSS HSGLEWRFFL YKKDAQALTK TSSNYSILTE NNDIQTDFFI SKNQHDFF G KKKWSLLFIW LTVLAFGVVM LGLYLGAPQL LGNFLAADIE SSTGIMLGVG VISLLYLLYS LPRYGVAYGI SYLIALILL AAGLFGAMYL ANFIFRIDQS TIQLIIFVYL FWLFFQARIG QTTIWTYCYW FKRSLKDRVF VKNLFNDNVN SQWRLDLIGS SVLILLFIV YAAFNFGGIN GTINLVIFYL IAIVALFSVF VNGLPLFSFG LINGWLSPYN YVQIHITLRH KKQMFKEVDQ I EEQLISGI NSF

UniProtKB: Uncharacterized protein MG277 homolog

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Macromolecule #2: SecE

MacromoleculeName: SecE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 14.489404 KDa
SequenceString:
MEKKKLPFGL KNKEKLTAYN DEKIHELHRQ LKAKIEAKKA KEKQDSKTKD TDKKVDQTPK VKVPFTKKFS NLWFGIDKEV NKIVWVTSK KLITIFLLIV LVSAIMIGIY FGINHLFIAL GVFKGK

UniProtKB: Uncharacterized protein MG055 homolog

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Macromolecule #3: Probable protein-export membrane protein SecG

MacromoleculeName: Probable protein-export membrane protein SecG / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 8.352255 KDa
SequenceString:
MDAIQIVMFV MAILCLIIGL LLSNHGSTGG LASLSGQDLE IFRKTKDRGI VKILQITMFI LVVLFLILGL VFHFAL

UniProtKB: Probable protein-export membrane protein SecG

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Macromolecule #4: Protein translocase subunit SecY

MacromoleculeName: Protein translocase subunit SecY / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 52.003633 KDa
SequenceString: MQAKPTTAVK QKQNFGQRLF TLLRNRDFMI SFLITVVLLV LFRVLAIIPL PGIQVNQTGL DQNSNDFFSL FNLLGGGGLN QLSLFAVGI SPYISAQIVM QLLSTDLIPP LSKLVNSGEV GRRKIEMITR IITLPFALVQ SFAVIQIATN SGGGSSPITL K NNGSDFVA ...String:
MQAKPTTAVK QKQNFGQRLF TLLRNRDFMI SFLITVVLLV LFRVLAIIPL PGIQVNQTGL DQNSNDFFSL FNLLGGGGLN QLSLFAVGI SPYISAQIVM QLLSTDLIPP LSKLVNSGEV GRRKIEMITR IITLPFALVQ SFAVIQIATN SGGGSSPITL K NNGSDFVA FYIIAMTAGT YLSVFLGDTI SKKGIGNGIT LLILSGILAQ LPEGFIAAYS VLSGVVVTIN ATLTTAISFF IY FMAFVTL LFATTFITQE TRKIPIQQSG QGLVTESSAL PYLPIKVNSA GVIPVIFASS IMSIPVTIAQ FQPQTESRWF VED YLSLSK PTGIVLYGIL VILFSFFYSY IQINPERLAK NFEKSGRFIP GIRPGKDTEK HIARVLVRIN FIGAPFLTVI AIIP YIVSA LIHLPNSLSL GGTGIIIIVT AVVEFMSALR SAATATNYQQ LRRNLAIEVQ KTAQQDKEEQ LRAETPGIGN LW

UniProtKB: Protein translocase subunit SecY

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Macromolecule #5: Uncharacterized lipoprotein MG309 homolog

MacromoleculeName: Uncharacterized lipoprotein MG309 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 143.385078 KDa
SequenceString: CAQPTASTVE GLFKPSSAFA DRTDFSLSSI LQKSLINRES FNQYLAMRLA PVLRTFYEDN YDTDIKERLN GFTADTDNAF VSQEQNLRN QFRENYLVHL QTDIFDNTGG NQAAWKLRDV NNKIIDDFIS RIFAKNFVEY VQDGVGPLTK PTKSLIENTS N FKNIKLQP ...String:
CAQPTASTVE GLFKPSSAFA DRTDFSLSSI LQKSLINRES FNQYLAMRLA PVLRTFYEDN YDTDIKERLN GFTADTDNAF VSQEQNLRN QFRENYLVHL QTDIFDNTGG NQAAWKLRDV NNKIIDDFIS RIFAKNFVEY VQDGVGPLTK PTKSLIENTS N FKNIKLQP KFVNKNAKLK INNDAVYAAI QDKLLDQFIT NENPNLVSRV VFTNETPVDG FDNYFNTKVI QSPTPSYQFQ VF NKYNQQS GGTKGANGFN LLASNLKSYK NDQSKGIDIP NKFSSDSGGK LLLKASDMFD TFDPSFSAAF IQGYLALQKK SKG ADSKEV DSLIKDKSII ENFFVDNNTQ AAAAARAASS SSEGTIQLKT ASDGGGTTQS TVHKTDLVKI FGDKDVFAGE YKQQ IGNTN ANQTGGGGSG GGGGTSTGSS TGSSTETTTG NSSKAVVDLI EVKKDSSSQP DYILSRGKDG IHLMAVDGGS HYLTE SGRD VAKQKKFLLF RALQTKYGLV DTDTTYDFKL FDEVKKYFDT NRILFLFEAL LDLSSDTNNK DNFLSYPQFK KFADSI KSI EKDLKELVQA HYKQAVFNET AVAENKVTLK LAERNQPFID NERNNQIEQN GLAAKLPYEQ DAKTGHYNDL GNYYKDI ID NVDKKGTSTV KTTSSNTGQT KNFSEEVVSK LKDNKKKVEE AAKKHVEALK VFTIPSPLYS QVILVQTKLS FTPESTSL G LNLALNNYLT STELQNSIKL SYFQEDEAFK KIIDITNLTF SQQSGGTGGT NGNNNLTADN WKIFKETYLL DLFESQAQK SIFGHVGSSD KNSSTKTGIE GVLDTLYSSL NLEERLDSDD VIDYLSYLYT AHWLLKDNLK NYKQSLQSKL SRTSNAFLVW SVDSEKNKN DSQSTLSSTA SSTSNTGLIQ LRSVVSLAQN QAAGQGGDNN SDITQTEVKN PNFVFGSSVY DWTNSKTPEV N RAADDTSS FFYTKSSSSS TGAAQSSATV LRSLNQASGM TTKTAKNRYG FRGIVTSSTS GSLPEAVSRR LFKQFVNQTE KG VKVGGQM LITTAKSGKA TLVLKQQADD AESTTNNAYK GALFSFGSMD NLKNIINGIQ TQTEFDALYN HLTSDLNIDV TGV DKNKTL TEQKTSLTSF VDSNFKQSTQ SAQRGDTSAR SARSATVQIK KTQEDNQNTN YKDVFSRFDG YIGDNKVEEK NYTS YQFLS DGGKYHATFV KQVNLDDVEK IGTDSLKQED SSKDKRLNLS LEEFLAAIAL EALDPNNQTQ AINALISGNK KGLVK VGDF RIFSSISAQW VRRF

UniProtKB: Uncharacterized lipoprotein MG309 homolog

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Macromolecule #6: Uncharacterized lipoprotein MG338 homolog

MacromoleculeName: Uncharacterized lipoprotein MG338 homolog / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 140.427859 KDa
SequenceString: CSALNTSNLF PRQNRSKQLI GFTENNIIKP EAVLKAALAE DNGTETILRV NFGEALKSWY QNNKDRNIAT RLTIFSENVE DEHDNLLDQ KQQAEPINWP IELQKEYDQW GGSESSWKAL KLYDRLIADF QSLIFSNIVA NVQLTDGSDQ FKPTTKDNLD S TSNKIKFV ...String:
CSALNTSNLF PRQNRSKQLI GFTENNIIKP EAVLKAALAE DNGTETILRV NFGEALKSWY QNNKDRNIAT RLTIFSENVE DEHDNLLDQ KQQAEPINWP IELQKEYDQW GGSESSWKAL KLYDRLIADF QSLIFSNIVA NVQLTDGSDQ FKPTTKDNLD S TSNKIKFV NSKPNDPNGE FFANLQAYLF AQWVVEENPL PLTQAFFAYQ APKDGLDSLY DQAAIGSALQ LGYAFPAFRE PN NGQSQGK TTFDPTPNSA QNFGDFIKAV FPEQKNGQTQ QSNTSSRTGL FDWQTKWNTN GAANKLLVTK SNLRGAFKGV GLA TAIIDQ YEYLVGGSKT SSLPEVKVDS NKSNQNPLDS FFMEGKDAVA IRSIVSRAKI AMTDQTPGFK VNPAFVKVKQ SQQN DTFYQ NQRKLSGGQS GDNNSQGKHH YLQDAVRLTS SQAMAAASTG ADSSSGTNVG GSSGGNSVLI PLPRSAALTH TQQQV QQTT STLQTPVYAR GDDGTYALAI DGGDYFLANN KRDFTKQADI LLYRYLQAKS NNFKENGVEF SLNLLESGSL FQTWAQ TGL TAKLYGALVA MMGSGQGTQV KGSVQGSSRA ASVSVQTTQQ NRQQSTDTQE SEVVKLAKSL LKSSADLAKP FTDNPTF KK ALTDIQSEYK DYLAAAGKLS EFKKDLGEVS GLQQAIIDRA DKYIQLEKQA QKSAIGLGQP LPYQRASDGS YPALEKFF I PEDSAADGKV KASESGSAAL VTLKTTDSQK STNTVKQPDI KPTRENNDKK LKQLTSDVET KASSLITKWG ATPQIGSQF SEIVSLKSKD NKPQTNMILA LLSDVGIKWT KILNSFKEWF FTNTNDFKNN YDSEKKELKG NEYKDFNDLV KQTLYLRSWQ RLTSKEKFG YYKELGSVKA QAAQSGMVSL SSSAAVANAV ASSGMQKSGD QTLLELGKKA FESELEASSS DGQYKYLRFL S TLMWLVKD GAKNYKRLLQ QAITVGTRAF VSWTVSYDDT ATASAAAAKA QVAVLKTAQA TNTQSDNPFN KFVQNPDYVQ GS ETNWFND KSTPIKPDSL LESESTYNFT AEPFDDKTKS QKRSTGGTTN EKHFFGFNGL TINSPQSVST ASAGLTEQIF NNF GQLVTS SDKSGALSQY KDKATLKRLI QNTNSDAELN AFGEVLHRAV NVDTSNLGRF NSSGEPLISF DNKKKFLVDV VDKL DDVYF NKFEGYVGQT KVKMSDSSSS SQGTKTIRKP KPHHSPRTRV SRLWAMSFRL PTRTLTKFLL VEKLIRTVL

UniProtKB: Uncharacterized lipoprotein MG338 homolog

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Macromolecule #7: Uncharacterized lipoprotein MG307 homolog

MacromoleculeName: Uncharacterized lipoprotein MG307 homolog / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 136.216672 KDa
SequenceString: CATPSNSALQ TVFKARSSQF FNGEQGSLQS ALTTALKNPV ANKQFIAAPL LKALEAWYEN NEDKKITQFL KDTKSNVDSQ YTTAVDKVV SASRNKSLFV QQDLLDNAGG SEATWKAQKL LEQLISDFAS RVFQKNYLNY KKDGQVSTGP FTYDELHKEE S WKNFEFSA ...String:
CATPSNSALQ TVFKARSSQF FNGEQGSLQS ALTTALKNPV ANKQFIAAPL LKALEAWYEN NEDKKITQFL KDTKSNVDSQ YTTAVDKVV SASRNKSLFV QQDLLDNAGG SEATWKAQKL LEQLISDFAS RVFQKNYLNY KKDGQVSTGP FTYDELHKEE S WKNFEFSA PRFSETNDDF FAKIQSQVFD QWVEYTDPTL ISQVNYKYSA PSQGLGQIYN REKLKDKLTP SYAFPFFAEE KD IAPNQNV GNKRWKQLVK GEGAITDNNI GQSGTNSQKT GLLKYRNESN KGDFLDFPLN LSDTNETKQL VDASNIVDQL EAA NLGAAL NLKLQVFEQD NDELPQIKEL KEDLNNTIVV DKSKDVEKAS KTNALFYNDQ EGKQQQSDSD PIAGALDDIF AQNT SEGTN LSKLAEQVKK AAATKMEAKT AVLRTNNSKG QQNNYVVLDA AIPTFNSTTS KSKNNSASNE VLVALKSGSI NLRQV QQTD QNSYSPIKFR IVRNSTGVTV FGLDGGSYYL KQDSTNKKSV SKQSLTLLTK SSSGNSNKVL RDLDKQKQFL KFRAFQ AKT NTFYSTNFAF SFPLNETLKS WFDKHRELIL ANALVNASLD QKDKASKALT EAFNPYKELI KEFAPVALAT TMISFYF DQ MKALNNKLLE RARNLNQNVN QANPTPWLNG LSAKLPYVNT NGNYEKLNNY FTFLITKTLW PKVGQEETSI SEESNKLK T KTADVDKIRD KILENIQTKV NDFVKNKLKP ALAPRPAYSN VILLNVNNDK VLSSGANWSL ASLLQSDKVN PLSFMLLKQ AFDNNDLFKK AQKLFKDIQE KSSNNGGMQS SSTTNSDADA LSKVIGNYYY TTWAKLTDKS IYGNPKDNKF DELFKLAFEA SIDEKSFNV DYKAVIDHYR FIYTLQWLVD QKLKNFKSLL KTNLKFGEVA FIAYKNTETT NFSNPQGVFG SYFNYENSAS E VKESTQTL DPNNFFYKTT TKPTVQAIQQ VASLALVQKQ QMQQNSTDHY GFTGLSTSTS SMFDASSRDA ILQQITKTSL QQ YGSKDQL KKIIQGTNNQ LLLDRIAVQL SGLNPSTTNG GSGKTIATYF QVDAVGNPTL DFQAKRKLLL DLLDQYQNYF GNG AQKSQR DSTPSGTGNY LTYQNGSDKY TYTQFTYQDI DSLSLTTTSG TNNKIASDVV AALLLFQAAD KGTQQLALSA INKP QLNIG DKRIESGLKL LK

UniProtKB: Uncharacterized lipoprotein MG307 homolog

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number subtomograms used: 1001
ExtractionNumber tomograms: 183 / Number images used: 6103 / Reference model: Data-driven, Iteratively improved
Method: Manual picking and Deep-learning based particle picking
Software - Name: Warp (ver. 1.0.9)
Details: 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 ...Details: 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.
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 5 / Avg.num./class: 1500
Details: Classification divided into two main classes, one corresponding to the open conformation (This class) and the other corresponding to the closed conformation.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial 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.
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9slf:
Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells

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