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- EMDB-79007: LPT translocon complex from Flavobacter johnsoniae built in compo... -

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Basic information

Entry
Database: EMDB / ID: EMD-79007
TitleLPT translocon complex from Flavobacter johnsoniae built in composite volume
Map datacomposite volume
Sample
  • Complex: LPT complex
    • Protein or peptide: Hypothetical lipoprotein
    • Protein or peptide: OstA family protein
    • Protein or peptide: Porin
    • Protein or peptide: Hypothetical lipoprotein
    • Protein or peptide: Outer membrane protein beta-barrel domain-containing protein
    • Protein or peptide: Hypothetical lipoprotein
    • Protein or peptide: DUF5683 domain-containing protein
    • Protein or peptide: Organic solvent tolerance protein OstA-like protein
    • Protein or peptide: Hypothetical lipoprotein
  • Ligand: alpha-D-galactopyranose
KeywordsLPS transport SLP transport outer membrane protein complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


glycolipid transfer activity / transporter complex / outer membrane / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / outer membrane-bounded periplasmic space
Similarity search - Function
Putative porin-10 / Domain of unknown function DUF5683 / Protein of unknown function DUF6452 / LPS-assembly protein LptD, central domain / Protein of unknown function DUF6048 / OstA-like protein / Putative porin / Family of unknown function (DUF5683) / Domain of unknown function (DUF6048) / LptD protein ...Putative porin-10 / Domain of unknown function DUF5683 / Protein of unknown function DUF6452 / LPS-assembly protein LptD, central domain / Protein of unknown function DUF6048 / OstA-like protein / Putative porin / Family of unknown function (DUF5683) / Domain of unknown function (DUF6048) / LptD protein / Family of unknown function (DUF6452) / SbsA, Ig-like domain / : / Bacterial Ig-like domain / : / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Organic solvent tolerance protein OstA-like protein / OstA family protein / Hypothetical lipoprotein / Hypothetical lipoprotein / Outer membrane protein beta-barrel domain-containing protein / Porin / Hypothetical lipoprotein / Hypothetical lipoprotein / DUF5683 domain-containing protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLea SM / Berks BC
Funding support United States, European Union, 3 items
OrganizationGrant numberCountry
Other private United States
European Research Council (ERC)101201241European Union
European Research Council (ERC)833713European Union
CitationJournal: To Be Published
Title: An expanded LPS translocon mediates surface lipoprotein export in the Bacteroidota
Authors: Liu X / Orenday Tapia L / Bryant OJ / Lea SM / Berks BC
History
DepositionSep 9, 2026-
Header (metadata) releaseOct 21, 2026-
Map releaseOct 21, 2026-
UpdateOct 21, 2026-
Current statusOct 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79007.png

Downloads & links

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Map

FileDownload / File: emd_79007.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 380 pix.
= 499.7 Å		1.32 Å/pix.
x 380 pix.
= 499.7 Å		1.32 Å/pix.
x 380 pix.
= 499.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.315 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.008844649 - 4.214985
Average (Standard dev.)0.00089275144 (±0.028252412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 499.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : LPT complex

EntireName: LPT complex
Components
  • Complex: LPT complex
    • Protein or peptide: Hypothetical lipoprotein
    • Protein or peptide: OstA family protein
    • Protein or peptide: Porin
    • Protein or peptide: Hypothetical lipoprotein
    • Protein or peptide: Outer membrane protein beta-barrel domain-containing protein
    • Protein or peptide: Hypothetical lipoprotein
    • Protein or peptide: DUF5683 domain-containing protein
    • Protein or peptide: Organic solvent tolerance protein OstA-like protein
    • Protein or peptide: Hypothetical lipoprotein
  • Ligand: alpha-D-galactopyranose

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Supramolecule #1: LPT complex

SupramoleculeName: LPT complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)

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Macromolecule #1: Hypothetical lipoprotein

MacromoleculeName: Hypothetical lipoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 65.414902 KDa
SequenceString: MFKSKFKYIS FLLVLLMMSC AKRGSITGGL KDTLAPVLVS SAPKNFTTDF KGNEINLVFD EYIKLKNLNK QLIISPPMKY EPLITPTGV SKFINIKIKD TLLPNTTYSF NFGESIADNN EGNALNQFKY IFSTGPYIDS LTLGGKIKDA YAKNVDNFVS V MLYEANYK ...String:
MFKSKFKYIS FLLVLLMMSC AKRGSITGGL KDTLAPVLVS SAPKNFTTDF KGNEINLVFD EYIKLKNLNK QLIISPPMKY EPLITPTGV SKFINIKIKD TLLPNTTYSF NFGESIADNN EGNALNQFKY IFSTGPYIDS LTLGGKIKDA YAKNVDNFVS V MLYEANYK YKDSVIYKEF PRYITNTLDS MRTFKFENLK EGKYLLVALK DKSNNNKYNP KDDKIGFIKH FITVPNDTLF EL SLFKETL PLKTLKPIQA SGNRLLLPYE GKQNFKLNKP TIVLKNNGET LETIVTQFPK KDSLQIWYKP LKADSLSLEV SKD TYNKKF TFKIKDQKKD TLNIKAVQNG VINFRDRFTL DTETPLVKFD KSKIKLINKD STAVDFTTEY NEFEQKLYVD FKKE PLEKY SFTFFPGALT DFYDKTNDTL SYKLSTKEYA DYGNLILNLK NVKRFPIIVE ITNKKGDEVL ASEYSEGKTQ IEFNL MLPS QFTIRVIYDD NKNKMYDTGN FLEKRYAEEV FYFQREIDVR TNWDVNETID LSVPYNPDVE KKEDLKKRKD DEKKRK AF

UniProtKB: Hypothetical lipoprotein

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Macromolecule #2: OstA family protein

MacromoleculeName: OstA family protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 62.401617 KDa
SequenceString: MLVLSVQSTF AQAAKSAKTA PKQIHVEHAD NFERNEPLVP GAVLLSGNVK VDHDGIVLTC NKAYIFEGEN YLKAFGNVQL VQGDTLFLN SKYAEYSGNL KQAFATGDAV MTSPDATLQT DTIHFDRNIQ QAYYNTKGTI VNKENTLVSK SGRYFAAEKK F QFLTEVTI ...String:
MLVLSVQSTF AQAAKSAKTA PKQIHVEHAD NFERNEPLVP GAVLLSGNVK VDHDGIVLTC NKAYIFEGEN YLKAFGNVQL VQGDTLFLN SKYAEYSGNL KQAFATGDAV MTSPDATLQT DTIHFDRNIQ QAYYNTKGTI VNKENTLVSK SGRYFAAEKK F QFLTEVTI TNPKYVIKSN HLDYYSNSGH TYLLGPSTIT SKANYIYTER GFYDTKKNLA HFLRKSYIKY DDRLIEGDSL YY NRNTEFA SATRNVKITD SINKGIVKGH YAEIFKLKDS MFVTKRAVAI NLVENDSVYI HGKKLMVTGK EGERILRAFN NVR FYKTDM SGKCDSIHSN SKTALTKLIG NPIIWNGESQ ITGDIMHLIG DNNTKKLDSL KVLNNTFIIS KDTLGTGYNQ VKGI NLFGK FKEGKLHDVD VIKNTEVVYF MRNDDNELIG INKNVSSKIN LILENNLIET ITFFNKVDGD IYPETDLPEN ARKLR GFVW RGDERIKSKD DIFTEEDNEL NEKLIKEGKE QEEKNKNVPL KVRKETLNYD KKKPAPKTEA KDKKK

UniProtKB: OstA family protein

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Macromolecule #3: Porin

MacromoleculeName: Porin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 76.868672 KDa
SequenceString: MRIFIFLYLL IIPTLLFSQE KTTSKGSLDM NTKYSSITDT VKKKKAKIAK IEQYQIISLE HDTINADTSL TIKSAYKQNH LRKDLFGLL EFPNIGQPLN ILQYSLTSYS PYPEIGFTAK HYNYIQADEI RYYSVPTPLT ELFFNTTINK GQNVDSFITL N TSKNLNFS ...String:
MRIFIFLYLL IIPTLLFSQE KTTSKGSLDM NTKYSSITDT VKKKKAKIAK IEQYQIISLE HDTINADTSL TIKSAYKQNH LRKDLFGLL EFPNIGQPLN ILQYSLTSYS PYPEIGFTAK HYNYIQADEI RYYSVPTPLT ELFFNTTINK GQNVDSFITL N TSKNLNFS IAYRGLRSEG DYINQLVSAG NFRFTTSYAT TNRRYALNVH YTYQDNLNEE NGGITTAEDF ESGSADFKNR QR LQVYLTD AKSFLKGRRL FFDHAFRINP KDGNNNLYIN HQFNYENKFF EYNQATVLSA VDGFTEPVKR FGESYVTSGI NDQ THFERL YNRVGAAYEN SLLGKFNFFV DDYRSNYKYN RILIDASGNV IPDNLFLQIN NFGGQYEYQK NKWNGRFLYT RSIT NQSLS DLDAKLRYDL NDKIQFDFRY RNINKLPNNN YNLYQSSYVE YNWSNNFKNE KINSLGASIS TPWVNAEAQY TVLKD HLYF VDMATPAQAA LRTQIVKPAQ YGNVINYLEI KASREFKFGK FALDNTLLYQ KVDQSELILN VPDFVTRNTF YYTNYF FKK ALYAQGGVVF NYFTKYYGNS YNPVIGEFFV QNTKEIGNYA TFDVFINARI RQTRFYLKAE HLNALFSSSN YYSAPDN PY RDFVIRFGLV WNFFQ

UniProtKB: Porin

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Macromolecule #4: Hypothetical lipoprotein

MacromoleculeName: Hypothetical lipoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 36.815992 KDa
SequenceString: MKKYASLIFL AFLLNGCDDG DLTVDEINFD SVTPVSCTTF TENSLSTDPT IIYKLKTQEA FVLQLPQTNG LVNNNGTVTY DIDNSIYRV LYRAYNGAVA KDNICGTIPP SSPNVTEEWV GASGKIKIVS SQVPTTTDAN DSFRIEAYNH VITFENITFQ K PSGPQVQE ...String:
MKKYASLIFL AFLLNGCDDG DLTVDEINFD SVTPVSCTTF TENSLSTDPT IIYKLKTQEA FVLQLPQTNG LVNNNGTVTY DIDNSIYRV LYRAYNGAVA KDNICGTIPP SSPNVTEEWV GASGKIKIVS SQVPTTTDAN DSFRIEAYNH VITFENITFQ K PSGPQVQE IFEFGTFKTT VTPADLTFQN TDTGEAFNCP DNKKIYNYNA SFTLTVENLD PALLTNEATA PNQPRSQAIT AT TNKVVYR NFVNGSGSIT STYDFCAAQI PSLPLLNQTW IGADTSETKK ATIEVTTEKI GDKTFIHTVV LKNVKLTKDS SYF QLGNTF TLGKITVNL

UniProtKB: Hypothetical lipoprotein

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Macromolecule #5: Outer membrane protein beta-barrel domain-containing protein

MacromoleculeName: Outer membrane protein beta-barrel domain-containing protein
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 31.259643 KDa
SequenceString: MKHTLKYTFS LCFLLSMFLG YSQVVIKDTV TVRDLDDQKP KTEVAAKPSV KEIKKDSISI KTDRYGLRVG VDLYKLTRGF YDKNYKGIE FTADWRLTKK YYIAAELGFE DKTTDDDRLN STATGTYIKG GFDYNLYDNW LDMENLITIG LRGGFSSFSQ D LNSYKIYN ...String:
MKHTLKYTFS LCFLLSMFLG YSQVVIKDTV TVRDLDDQKP KTEVAAKPSV KEIKKDSISI KTDRYGLRVG VDLYKLTRGF YDKNYKGIE FTADWRLTKK YYIAAELGFE DKTTDDDRLN STATGTYIKG GFDYNLYDNW LDMENLITIG LRGGFSSFSQ D LNSYKIYN PNPYWGEQPA MSANQKYNGL SAAWLEVALG VKAKVFNNIF VGFGVQLKLL AMNNKPSGFD NLYIPGFNRT YD GSFGVGF NYTVSYFIPI YKKKTIVPEI INQAPKK

UniProtKB: Outer membrane protein beta-barrel domain-containing protein

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Macromolecule #6: Hypothetical lipoprotein

MacromoleculeName: Hypothetical lipoprotein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 20.10465 KDa
SequenceString:
MKKIISLLLL FTFGLSSCEK DDICDANTPT TPRLVITFYD NAAPTSLKTV TNLKVVGEGK EDTDAIIFNE TGTSVTKYLT NANTISIPL KTDAKTTTYK FIYNATSATP NIDVLTFNYE TQSVYVSRAC GFKTTFTLNP RDNTANSGLI RTDPAGDGLW M LNINVVNS NIELENETHV KVYF

UniProtKB: Hypothetical lipoprotein

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Macromolecule #7: DUF5683 domain-containing protein

MacromoleculeName: DUF5683 domain-containing protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 21.526623 KDa
SequenceString:
MNKIVPISLL FFLLGTVSLF AQVKEETVLV AKDSIALEEI DPLTPAKAAF YSAILPGLGQ AYNKKYWKIP LVYGAIGTSL YFYIDNNNK YRDYRNAYKR RLEGYNDDKY QYLDESRLVA GQKFYQRNRD LSALFVVGFY VLNIIDANVD AALIQFNVNE R LSMRPEIY PNDVTFKPNV GLTFNYRF

UniProtKB: DUF5683 domain-containing protein

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Macromolecule #8: Organic solvent tolerance protein OstA-like protein

MacromoleculeName: Organic solvent tolerance protein OstA-like protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 104.330469 KDa
SequenceString: LHTNLFNIVL ISFFLTIGCG KSYSQEIKPK KKSLPASAWS HPQFEKGGGS GGGSGGSAWS HPQFEKTSVK QTNKPATAPA AATPAVSTA TVDTIKIDSI KPKKQFLDAP TKYKAKDYAK YDKKNKLLTL YNEAELYYKD VELKSGIIIL NLEKDEVYAG R IKDSAGVL ...String:
LHTNLFNIVL ISFFLTIGCG KSYSQEIKPK KKSLPASAWS HPQFEKGGGS GGGSGGSAWS HPQFEKTSVK QTNKPATAPA AATPAVSTA TVDTIKIDSI KPKKQFLDAP TKYKAKDYAK YDKKNKLLTL YNEAELYYKD VELKSGIIIL NLEKDEVYAG R IKDSAGVL VQYPNFKQGT NEVQPDSIRF NFKTKKALIY NSRTKQGELN IKASVTKKEN DSVYFLKGAR ITTAQDIDNP EY YFQTSRI KFVPGKKIVA GLTQMVIADV PTPLALPYGF FPLSKEKSVS GIIIPSYNDS NTRGFSLQNG GYYFALSDNY DLT VLGDYY TNGSYAMRFE SAYAKRYKYR GNINVRFENL INSERGYPDY SKQNIYNIQW SHSKDTKSNP NSTFSASVNM GSSK YFKRS INQANIGSNL NNTLSSSISY NKTFNTIPGS RISLSATHQQ NTQTEEILMT LPNFQGSIDR IYPFVGENGV KKGFF KNIN LQYNVTGKNN FKTTDSLFFK PQMFRDAQIG MQHSIPISTN FKIFKYFSAG ASTNYQETWV TKTIDKNYDA SKGQVA STT VNGFDAFRTY NFSTNLGTTI YGTFNFGTDK KIQSIRHVMR PSITYSYTPS FERYYDHYTV DAAGRISTDE YTRFENG IY GAPGKENSNI VGFSLSNTFE AKVRDSDSTK TEPKKIMLLN NLNFSTSYNF NANGKETLAW QPIIVSGGTQ FFENKMNV N FGAVLNPYAI DNAGNVINMY NIENGGSLFR MTSANITMNY SFSNKGTGKE KNTQSQRNGG RNDDLFGTNT DLNDSRNSQ FANDPDREED VITEFFSSKL PWDMTMAYSL TYSNANRENK ITGNSIMISA NMDITPKWKG GVSTGFDFVQ KGVTFTQFRF ERDLLSWRM AFNWQPMGTS SNWNFFIGIK SGMLSDIKWN KRSTINR

UniProtKB: Organic solvent tolerance protein OstA-like protein

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Macromolecule #9: Hypothetical lipoprotein

MacromoleculeName: Hypothetical lipoprotein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 19.251713 KDa
SequenceString:
MKHLKYLLLL LVATTFSGCG VYNFTGASPI DAKTFQVSFF HNNADLVEPG IDRDFTLALQ DLIMNQTNLN LVSNGGELAY EGEIVDYRI TPMTATAVTS TGDVGAAQNR LTIRINVRFT NKKKETDDFE KPFEFYYDFP GASLPTGSVL NEAIKTIFER I TQDIFNES LAKW

UniProtKB: Hypothetical lipoprotein

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Macromolecule #12: alpha-D-galactopyranose

MacromoleculeName: alpha-D-galactopyranose / type: ligand / ID: 12 / Number of copies: 6 / Formula: GLA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GLA:
alpha-D-galactopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
DetailsData were collected at both 200kV and 300kV on two different Titan Krios and an Arctica
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Details: Data were collected on three microscopes Titan Krios / Gatan K3 BioQuantum Titan Krios / Falcon 4i Arctica / Gatan K3 BioQuantum
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsData were combined from two different Gatan K3 Bioquantum detectors and a Falcon 4i
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: The volume is a composite volume - the numbers of particles used for the different components varied from 218,874 to 70,401 particles Resolution varied from 2.9 to 3.5
Number images used: 218874
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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