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- EMDB-54992: 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-54992
TitleOpen conformation dome complex including the Sec-translocon (SecYEG-SecDF) from untreated Mycoplasma pneumoniae cells
Map dataOpen dome complex from untreated Mycoplasma pneumoniae cells. Post processing in RELION
Sample
  • Cell: Open conformation dome complex including the Sec-translocon (SecYEG-SecDF) from untreated Mycoplasma pneumoniae cells
    • Protein or peptide: Major dome-forming protein (Mdp) 444, previously MPN444
    • Protein or peptide: Major dome-forming protein (Mdp) 436, previously MPN436
    • Protein or peptide: Major dome-forming protein (Mdp) 489, previously MPN489
    • Protein or peptide: MPN523
    • Protein or peptide: SecY
    • Protein or peptide: SecE
    • Protein or peptide: SecG
    • Protein or peptide: SecDF
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
: / Family of unknown function (DUF6856) / 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 ...: / Family of unknown function (DUF6856) / 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 MG348 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 309 (bacteria) / Mycoplasmoides pneumoniae M129 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 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 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54992.png

Downloads & links

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Map

FileDownload / File: emd_54992.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOpen dome complex from untreated Mycoplasma pneumoniae cells. Post processing in RELION
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 112 pix.
= 380.912 Å		3.4 Å/pix.
x 112 pix.
= 380.912 Å		3.4 Å/pix.
x 112 pix.
= 380.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.401 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.329
Minimum - Maximum-0.46311295 - 0.9003766
Average (Standard dev.)0.017774863 (±0.1504333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions112112112
Spacing112112112
CellA=B=C: 380.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54992_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54992_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54992_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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-SecDF) from untreated Mycoplasma pneumoniae cells
Components
  • Cell: Open conformation dome complex including the Sec-translocon (SecYEG-SecDF) from untreated Mycoplasma pneumoniae cells
    • Protein or peptide: Major dome-forming protein (Mdp) 444, previously MPN444
    • Protein or peptide: Major dome-forming protein (Mdp) 436, previously MPN436
    • Protein or peptide: Major dome-forming protein (Mdp) 489, previously MPN489
    • Protein or peptide: MPN523
    • Protein or peptide: SecY
    • Protein or peptide: SecE
    • Protein or peptide: SecG
    • Protein or peptide: SecDF

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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-SecDF) from untreated Mycoplasma pneumoniae cells
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides pneumoniae 309 (bacteria)

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Macromolecule #1: Major dome-forming protein (Mdp) 444, previously MPN444

MacromoleculeName: Major dome-forming protein (Mdp) 444, previously MPN444
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
SequenceString: CAQPTASTVE GLFKPSSAFA DRTDFSLSSI LQKSLINRES FNQYLAMRLA PVLRTFYEDN YDTDIKERLN GFTADTDNAF VSQEQNLRNQ FRENYLVHLQ TDIFDNTGGN QAAWKLRDVN NKIIDDFISR IFAKNFVEYV QDGVGPLTKP TKSLIENTSN FKNIKLQPKF ...String:
CAQPTASTVE GLFKPSSAFA DRTDFSLSSI LQKSLINRES FNQYLAMRLA PVLRTFYEDN YDTDIKERLN GFTADTDNAF VSQEQNLRNQ FRENYLVHLQ TDIFDNTGGN QAAWKLRDVN NKIIDDFISR IFAKNFVEYV QDGVGPLTKP TKSLIENTSN FKNIKLQPKF VNKNAKLKIN NDAVYAAIQD KLLDQFITNE NPNLVSRVVF TNETPVDGFD NYFNTKVIQS PTPSYQFQVF NKYNQQSGGT KGANGFNLLA SNLKSYKNDQ SKGIDIPNKF SSDSGGKLLL KASDMFDTFD PSFSAAFIQG YLALQKKSKG ADSKEVDSLI KDKSIIENFF VDNNTQAAAA ARAASSSSEG TIQLKTASDG GGTTQSTVHK TDLVKIFGDK DVFAGEYKQQ IGNTNANQTG GGGSGGGGGT STGSSTGSST ETTTGNSSKA VVDLIEVKKD SSSQPDYILS RGKDGIHLMA VDGGSHYLTE SGRDVAKQKK FLLFRALQTK YGLVDTDTTY DFKLFDEVKK YFDTNRILFL FEALLDLSSD TNNKDNFLSY PQFKKFADSI KSIEKDLKEL VQAHYKQAVF NETAVAENKV TLKLAERNQP FIDNERNNQI EQNGLAAKLP YEQDAKTGHY NDLGNYYKDI IDNVDKKGTS TVKTTSSNTG QTKNFSEEVV SKLKDNKKKV EEAAKKHVEA LKVFTIPSPL YSQVILVQTK LSFTPESTSL GLNLALNNYL TSTELQNSIK LSYFQEDEAF KKIIDITNLT FSQQSGGTGG TNGNNNLTAD NWKIFKETYL LDLFESQAQK SIFGHVGSSD KNSSTKTGIE GVLDTLYSSL NLEERLDSDD VIDYLSYLYT AHWLLKDNLK NYKQSLQSKL SRTSNAFLVW SVDSEKNKND SQSTLSSTAS STSNTGLIQL RSVVSLAQNQ AAGQGGDNNS DITQTEVKNP NFVFGSSVYD WTNSKTPEVN RAADDTSSFF YTKSSSSSTG AAQSSATVLR SLNQASGMTT KTAKNRYGFR GIVTSSTSGS LPEAVSRRLF KQFVNQTEKG VKVGGQMLIT TAKSGKATLV LKQQADDAES TTNNAYKGAL FSFGSMDNLK NIINGIQTQT EFDALYNHLT SDLNIDVTGV DKNKTLTEQK TSLTSFVDSN FKQSTQSAQR GDTSARSARS ATVQIKKTQE DNQNTNYKDV FSRFDGYIGD NKVEEKNYTS YQFLSDGGKY HATFVKQVNL DDVEKIGTDS LKQEDSSKDK RLNLSLEEFL AAIALEALDP NNQTQAINAL ISGNKKGLVK VGDFRIFSSI SAQWVRRF

UniProtKB: Uncharacterized lipoprotein MG309 homolog

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Macromolecule #2: Major dome-forming protein (Mdp) 436, previously MPN436

MacromoleculeName: Major dome-forming protein (Mdp) 436, previously MPN436
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
SequenceString: CATPSNSALQ TVFKARSSQF FNGEQGSLQS ALTTALKNPV ANKQFIAAPL LKALEAWYEN NEDKKITQFL KDTKSNVDSQ YTTAVDKVVS ASRNKSLFVQ QDLLDNAGGS EATWKAQKLL EQLISDFASR VFQKNYLNYK KDGQVSTGPF TYDELHKEES WKNFEFSAPR ...String:
CATPSNSALQ TVFKARSSQF FNGEQGSLQS ALTTALKNPV ANKQFIAAPL LKALEAWYEN NEDKKITQFL KDTKSNVDSQ YTTAVDKVVS ASRNKSLFVQ QDLLDNAGGS EATWKAQKLL EQLISDFASR VFQKNYLNYK KDGQVSTGPF TYDELHKEES WKNFEFSAPR FSETNDDFFA KIQSQVFDQW VEYTDPTLIS QVNYKYSAPS QGLGQIYNRE KLKDKLTPSY AFPFFAEEKD IAPNQNVGNK RWKQLVKGEG AITDNNIGQS GTNSQKTGLL KYRNESNKGD FLDFPLNLSD TNETKQLVDA SNIVDQLEAA NLGAALNLKL QVFEQDNDEL PQIKELKEDL NNTIVVDKSK DVEKASKTNA LFYNDQEGKQ QQSDSDPIAG ALDDIFAQNT SEGTNLSKLA EQVKKAAATK MEAKTAVLRT NNSKGQQNNY VVLDAAIPTF NSTTSKSKNN SASNEVLVAL KSGSINLRQV QQTDQNSYSP IKFRIVRNST GVTVFGLDGG SYYLKQDSTN KKSVSKQSLT LLTKSSSGNS NKVLRDLDKQ KQFLKFRAFQ AKTNTFYSTN FAFSFPLNET LKSWFDKHRE LILANALVNA SLDQKDKASK ALTEAFNPYK ELIKEFAPVA LATTMISFYF DQMKALNNKL LERARNLNQN VNQANPTPWL NGLSAKLPYV NTNGNYEKLN NYFTFLITKT LWPKVGQEET SISEESNKLK TKTADVDKIR DKILENIQTK VNDFVKNKLK PALAPRPAYS NVILLNVNND KVLSSGANWS LASLLQSDKV NPLSFMLLKQ AFDNNDLFKK AQKLFKDIQE KSSNNGGMQS SSTTNSDADA LSKVIGNYYY TTWAKLTDKS IYGNPKDNKF DELFKLAFEA SIDEKSFNVD YKAVIDHYRF IYTLQWLVDQ KLKNFKSLLK TNLKFGEVAF IAYKNTETTN FSNPQGVFGS YFNYENSASE VKESTQTLDP NNFFYKTTTK PTVQAIQQVA SLALVQKQQM QQNSTDHYGF TGLSTSTSSM FDASSRDAIL QQITKTSLQQ YGSKDQLKKI IQGTNNQLLL DRIAVQLSGL NPSTTNGGSG KTIATYFQVD AVGNPTLDFQ AKRKLLLDLL DQYQNYFGNG AQKSQRDSTP SGTGNYLTYQ NGSDKYTYTQ FTYQDIDSLS LTTTSGTNNK IASDVVAALL LFQAADKGTQ QLALSAINKP QLNIGDKRIE SGLKLLK

UniProtKB: Uncharacterized lipoprotein MG307 homolog

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Macromolecule #3: Major dome-forming protein (Mdp) 489, previously MPN489

MacromoleculeName: Major dome-forming protein (Mdp) 489, previously MPN489
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
SequenceString: CSALNTSNLF PRQNRSKQLI GFTENNIIKP EAVLKAALAE DNGTETILRV NFGEALKSWY QNNKDRNIAT RLTIFSENVE DEHDNLLDQK QQAEPINWPI ELQKEYDQWG GSESSWKALK LYDRLIADFQ SLIFSNIVAN VQLTDGSDQF KPTTKDNLDS TSNKIKFVNS ...String:
CSALNTSNLF PRQNRSKQLI GFTENNIIKP EAVLKAALAE DNGTETILRV NFGEALKSWY QNNKDRNIAT RLTIFSENVE DEHDNLLDQK QQAEPINWPI ELQKEYDQWG GSESSWKALK LYDRLIADFQ SLIFSNIVAN VQLTDGSDQF KPTTKDNLDS TSNKIKFVNS KPNDPNGEFF ANLQAYLFAQ WVVEENPLPL TQAFFAYQAP KDGLDSLYDQ AAIGSALQLG YAFPAFREPN NGQSQGKTTF DPTPNSAQNF GDFIKAVFPE QKNGQTQQSN TSSRTGLFDW QTKWNTNGAA NKLLVTKSNL RGAFKGVGLA TAIIDQYEYL VGGSKTSSLP EVKVDSNKSN QNPLDSFFME GKDAVAIRSI VSRAKIAMTD QTPGFKVNPA FVKVKQSQQN DTFYQNQRKL SGGQSGDNNS QGKHHYLQDA VRLTSSQAMA AASTGADSSS GTNVGGSSGG NSVLIPLPRS AALTHTQQQV QQTTSTLQTP VYARGDDGTY ALAIDGGDYF LANNKRDFTK QADILLYRYL QAKSNNFKEN GVEFSLNLLE SGSLFQTWAQ TGLTAKLYGA LVAMMGSGQG TQVKGSVQGS SRAASVSVQT TQQNRQQSTD TQESEVVKLA KSLLKSSADL AKPFTDNPTF KKALTDIQSE YKDYLAAAGK LSEFKKDLGE VSGLQQAIID RADKYIQLEK QAQKSAIGLG QPLPYQRASD GSYPALEKFF IPEDSAADGK VKASESGSAA LVTLKTTDSQ KSTNTVKQPD IKPTRENNDK KLKQLTSDVE TKASSLITKW GATPQIGSQF SEIVSLKSKD NKPQTNMILA LLSDVGIKWT KILNSFKEWF FTNTNDFKNN YDSEKKELKG NEYKDFNDLV KQTLYLRSWQ RLTSKEKFGY YKELGSVKAQ AAQSGMVSLS SSAAVANAVA SSGMQKSGDQ TLLELGKKAF ESELEASSSD GQYKYLRFLS TLMWLVKDGA KNYKRLLQQA ITVGTRAFVS WTVSYDDTAT ASAAAAKAQV AVLKTAQATN TQSDNPFNKF VQNPDYVQGS ETNWFNDKST PIKPDSLLES ESTYNFTAEP FDDKTKSQKR STGGTTNEKH FFGFNGLTIN SPQSVSTASA GLTEQIFNNF GQLVTSSDKS GALSQYKDKA TLKRLIQNTN SDAELNAFGE VLHRAVNVDT SNLGRFNSSG EPLISFDNKK KFLVDVVDKL DDVYFNKFEG YVGQTKVKMS DSSSSSQGTK TIRKPKPHHS PRTRVSRLWA MSFRLPTRTL TKFLLVEKLI RTVL

UniProtKB: Uncharacterized lipoprotein MG338 homolog

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Macromolecule #4: MPN523

MacromoleculeName: MPN523 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
SequenceString: CSNIDKPNVF RTLSQQSVEN KVDYSKLPKE NKTVRNLVFG TAEYNDGNYV LVVTTETDSS QINFLNGSNN QAVSTENWAG DLGTTVKQVQ NRYSTYPKGV KFLIWNDIDP NPVKWNPFAR YPVIASDNEL AKQTDKDNSD KLRRNDESAI QYREIVTFIQ TVYSGSVNNL ...String:
CSNIDKPNVF RTLSQQSVEN KVDYSKLPKE NKTVRNLVFG TAEYNDGNYV LVVTTETDSS QINFLNGSNN QAVSTENWAG DLGTTVKQVQ NRYSTYPKGV KFLIWNDIDP NPVKWNPFAR YPVIASDNEL AKQTDKDNSD KLRRNDESAI QYREIVTFIQ TVYSGSVNNL INQSNVHAQT VGTDVTKAIV IAFRKNNLDQ ISAHFYNPDN SNGSNAPGSN QPNQDSGNNG STTPAAPAAA AAKKSYSAGS FGVKRHAVQV SINFLNFLDS VYTPLN

UniProtKB: Uncharacterized lipoprotein MG348 homolog

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Macromolecule #5: SecY

MacromoleculeName: SecY / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
SequenceString: MQAKPTTAVK QKQNFGQRLF TLLRNRDFMI SFLITVVLLV LFRVLAIIPL PGIQVNQTGL DQNSNDFFSL FNLLGGGGLN QLSLFAVGIS PYISAQIVMQ LLSTDLIPPL SKLVNSGEVG RRKIEMITRI ITLPFALVQS FAVIQIATNS GGGSSPITLK NNGSDFVAFY ...String:
MQAKPTTAVK QKQNFGQRLF TLLRNRDFMI SFLITVVLLV LFRVLAIIPL PGIQVNQTGL DQNSNDFFSL FNLLGGGGLN QLSLFAVGIS PYISAQIVMQ LLSTDLIPPL SKLVNSGEVG RRKIEMITRI ITLPFALVQS FAVIQIATNS GGGSSPITLK NNGSDFVAFY IIAMTAGTYL SVFLGDTISK KGIGNGITLL ILSGILAQLP EGFIAAYSVL SGVVVTINAT LTTAISFFIY FMAFVTLLFA TTFITQETRK IPIQQSGQGL VTESSALPYL PIKVNSAGVI PVIFASSIMS IPVTIAQFQP QTESRWFVED YLSLSKPTGI VLYGILVILF SFFYSYIQIN PERLAKNFEK SGRFIPGIRP GKDTEKHIAR VLVRINFIGA PFLTVIAIIP YIVSALIHLP NSLSLGGTGI IIIVTAVVEF MSALRSAATA TNYQQLRRNL AIEVQKTAQQ DKEEQLRAET PGIGNLW

UniProtKB: Protein translocase subunit SecY

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Macromolecule #6: SecE

MacromoleculeName: SecE / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
SequenceString:
MEKKKLPFGL KNKEKLTAYN DEKIHELHRQ LKAKIEAKKA KEKQDSKTKD TDKKVDQTPK VKVPFTKKFS NLWFGIDKEV NKIVWVTSKK LITIFLLIVL VSAIMIGIYF GINHLFIALG VFKGK

UniProtKB: Uncharacterized protein MG055 homolog

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Macromolecule #7: SecG

MacromoleculeName: SecG / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
SequenceString:
MDAIQIVMFV MAILCLIIGL LLSNHGSTGG LASLSGQDLE IFRKTKDRGI VKILQITMFI LVVLFLILGL VFHFAL

UniProtKB: Probable protein-export membrane protein SecG

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Macromolecule #8: SecDF

MacromoleculeName: SecDF / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
SequenceString: MGLKKRVSFD WLLKIGIILV LAFLGLFGII FGSYKLLNDS RLGVVFNGST TTTVYFLNHK SKDANKELDP TQKKDGNGSG NNTEMITDVN GFLNNIEKSY ANSLYAQGFS SVNITKNSHD TSAKELSDKG VFDSSWLVND GLPSISVTFE QRREEARTRA RKRQIDAQVK ...String:
MGLKKRVSFD WLLKIGIILV LAFLGLFGII FGSYKLLNDS RLGVVFNGST TTTVYFLNHK SKDANKELDP TQKKDGNGSG NNTEMITDVN GFLNNIEKSY ANSLYAQGFS SVNITKNSHD TSAKELSDKG VFDSSWLVND GLPSISVTFE QRREEARTRA RKRQIDAQVK RNALSAIEHN YKLSLETTDG IVLFDSFDKE FIRNSLTAVV PQTTNTNSAL TFEYKLSKNV ITKESLHNDF LDFIKSKSLT DSDYNTGNGQ KSVEGSGKWF KDKANGSAQN GNKTLVLWKD KEGAVQYVRN IFNVPKGGTD YLTFNEREKN LWDFLHAEGN FSSGDNLFLQ KNNNGNSPIT KASDITLKNI YYIYAAPTHF SQVATKDNNN KDAADVVAVA NSADTRKLRS GDATGFSGLF SNYILAEIRT EDPVAKNGDP VKVNATLQSF LDSNNQRLEH GGNIKFQVAN FVNNDGSYVP ASYLEASRVK VLLSNGFPET ATIAAANTKL VNAPLSNTLA RDVSNFASSF IALGVIILLA TIALGIRYKL LGLYKALALA LSAISSLAFF SAVGGVVDVF SFVGIFFVVA VNIINLITLA ELFLRNIKNN ASIVESWKLC LKRSFFTMIE THICWLLSAL VVIYLSNYQV QQLGTLMAVS AITSYFLNYG LGVILVWLFV SSHSGLEWRF FLYKKDAQAL TKTSSNYSIL TENNDIQTDF FISKNQHDFF GKKKWSLLFI WLTVLAFGVV MLGLYLGAPQ LLGNFLAADI ESSTGIMLGV GVISLLYLLY SLPRYGVAYG ISYLIALILL AAGLFGAMYL ANFIFRIDQS TIQLIIFVYL FWLFFQARIG QTTIWTYCYW FKRSLKDRVF VKNLFNDNVN SQWRLDLIGS SVLILLFIVY AAFNFGGING TINLVIFYLI AIVALFSVFV NGLPLFSFGL INGWLSPYNY VQIHITLRHK KQMFKEVDQI EEQLISGINS F

UniProtKB: Uncharacterized protein MG277 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: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
Details: Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental chamber..

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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 / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
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: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number subtomograms used: 177
ExtractionNumber tomograms: 355 / Number images used: 13770 / 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: 412 / Software - Name: RELION (ver. 4.0.1)
Details: Final 3D classification was focused on SecA seperating into two main classes consisting of a class with and one without SecA
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
RefinementProtocol: RIGID BODY FIT

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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