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- EMDB-79006: LPT translocon complex from Flavobacter johnsoniae - consensus volume -

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Basic information

Entry
Database: EMDB / ID: EMD-79006
TitleLPT translocon complex from Flavobacter johnsoniae - consensus volume
Map datarefinement volume
Sample
  • Complex: LPT complex
    • Protein or peptide: LptP
    • Protein or peptide: LptA
    • Protein or peptide: LptN
    • Protein or peptide: LptS
    • Protein or peptide: LptQ
    • Protein or peptide: LptR
    • Protein or peptide: LptT
    • Protein or peptide: LptD
    • Protein or peptide: LptE
KeywordsLPS transport SLP transport outer membrane protein complex / MEMBRANE PROTEIN
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79006.png

Downloads & links

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Map

FileDownload / File: emd_79006.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefinement 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: 0.31
Minimum - Maximum-0.7698096 - 1.9706506
Average (Standard dev.)0.0010094825 (±0.031320717)
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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Mask #1

Fileemd_79006_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: deepEMhanced volume

Fileemd_79006_additional_1.map
AnnotationdeepEMhanced volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_79006_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_79006_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LPT complex

EntireName: LPT complex
Components
  • Complex: LPT complex
    • Protein or peptide: LptP
    • Protein or peptide: LptA
    • Protein or peptide: LptN
    • Protein or peptide: LptS
    • Protein or peptide: LptQ
    • Protein or peptide: LptR
    • Protein or peptide: LptT
    • Protein or peptide: LptD
    • Protein or peptide: LptE

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Supramolecule #1: LPT complex

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

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Macromolecule #1: LptP

MacromoleculeName: LptP / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 60.591941 KDa
SequenceString: MFKSKFKYIS FLLVLLMMSC AKRGSITGGL KDTLAPVLVS SAPKNFTTDF KGNEINLVFD EYIKLKNLNK QLIISPPMKY EPLITPTGVS KFINIKIKDT LLPNTTYSFN FGESIADNNE GNALNQFKYI FSTGPYIDSL TLGGKIKDAY AKNVDNFVSV MLYEANYKYK ...String:
MFKSKFKYIS FLLVLLMMSC AKRGSITGGL KDTLAPVLVS SAPKNFTTDF KGNEINLVFD EYIKLKNLNK QLIISPPMKY EPLITPTGVS KFINIKIKDT LLPNTTYSFN FGESIADNNE GNALNQFKYI FSTGPYIDSL TLGGKIKDAY AKNVDNFVSV MLYEANYKYK DSVIYKEFPR YITNTLDSMR TFKFENLKEG KYLLVALKDK SNNNKYNPKD DKIGFIKHFI TVPNDTLFEL SLFKETLPLK TLKPIQASGN RLLLPYEGKQ NFKLNKPTIV LKNNGETLET IVTQFPKKDS LQIWYKPLKA DSLSLEVSKD TYNKKFTFKI KDQKKDTLNI KAVQNGVINF RDRFTLDTET PLVKFDKSKI KLINKDSTAV DFTTEYNEFE QKLYVDFKKE PLEKYSFTFF PGALTDFYDK TNDTLSYKLS TKEYADYGNL ILNLKNVKRF PIIVEITNKK GDEVLASEYS EGKTQIEFNL MLPSQFTIRV IYDDNKNKMY DTGNFLEKRY AEEVFYFQRE IDVRTNWDVN ETIDLSVPYN PDVEKKEDLK KRKDDEKKRK AF

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Macromolecule #2: LptA

MacromoleculeName: LptA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 42.206852 KDa
SequenceString: MLVLSVQSTF AQAAKSAKTA PKQIHVEHAD NFERNEPLVP GAVLLSGNVK VDHDGIVLTC NKAYIFEGEN YLKAFGNVQL VQGDTLFLNS KYAEYSGNLK QAFATGDAVM TSPDATLQTD TIHFDRNIQQ AYYNTKGTIV NKENTLVSKS GRYFAAEKKF QFLTEVTITN ...String:
MLVLSVQSTF AQAAKSAKTA PKQIHVEHAD NFERNEPLVP GAVLLSGNVK VDHDGIVLTC NKAYIFEGEN YLKAFGNVQL VQGDTLFLNS KYAEYSGNLK QAFATGDAVM TSPDATLQTD TIHFDRNIQQ AYYNTKGTIV NKENTLVSKS GRYFAAEKKF QFLTEVTITN PKYVIKSNHL DYYSNSGHTY LLGPSTITSK ANYIYTERGF YDTKKNLAHF LRKSYIKYDD RLIEGDSLYY NRNTEFASAT RNVKITDSIN KGIVKGHYAE IFKLKDSMFV TKRAVAINLV ENDSVYIHGK KLMVTGKEGE RILRAFNNVR FYKTDMSGKC DSIHSNSKTA LTKLIGNPII WNGESQITGD IMHLIGDNNT KKLDSLKVLN NTFIISKDTL GTGYNQVKGI NLFGKFKEGK LHDVDVIKNT EVVYFMRNDD NELIGINKNV SSKINLILEN NLIETITFFN KVDGDIYPET DLPENARKLR GFVWRGDERI KSKDDIFTEE DNELNEKLIK EGKEQEEKNK NVPLKVRKET LNYDKKKPAP KTEAKDKKK

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Macromolecule #3: LptN

MacromoleculeName: LptN / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 71.564312 KDa
SequenceString: MRIFIFLYLL IIPTLLFSQE KTTSKGSLDM NTKYSSITDT VKKKKAKIAK IEQYQIISLE HDTINADTSL TIKSAYKQNH LRKDLFGLLE FPNIGQPLNI LQYSLTSYSP YPEIGFTAKH YNYIQADEIR YYSVPTPLTE LFFNTTINKG QNVDSFITLN TSKNLNFSIA ...String:
MRIFIFLYLL IIPTLLFSQE KTTSKGSLDM NTKYSSITDT VKKKKAKIAK IEQYQIISLE HDTINADTSL TIKSAYKQNH LRKDLFGLLE FPNIGQPLNI LQYSLTSYSP YPEIGFTAKH YNYIQADEIR YYSVPTPLTE LFFNTTINKG QNVDSFITLN TSKNLNFSIA YRGLRSEGDY INQLVSAGNF RFTTSYATTN RRYALNVHYT YQDNLNEENG GITTAEDFES GSADFKNRQR LQVYLTDAKS FLKGRRLFFD HAFRINPKDG NNNLYINHQF NYENKFFEYN QATVLSAVDG FTEPVKRFGE SYVTSGINDQ THFERLYNRV GAAYENSLLG KFNFFVDDYR SNYKYNRILI DASGNVIPDN LFLQINNFGG QYEYQKNKWN GRFLYTRSIT NQSLSDLDAK LRYDLNDKIQ FDFRYRNINK LPNNNYNLYQ SSYVEYNWSN NFKNEKINSL GASISTPWVN AEAQYTVLKD HLYFVDMATP AQAALRTQIV KPAQYGNVIN YLEIKASREF KFGKFALDNT LLYQKVDQSE LILNVPDFVT RNTFYYTNYF FKKALYAQGG VVFNYFTKYY GNSYNPVIGE FFVQNTKEIG NYATFDVFIN ARIRQTRFYL KAEHLNALFS SSNYYSAPDN PYRDFVIRFG LVWNFFQ

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Macromolecule #4: LptS

MacromoleculeName: LptS / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 35.002754 KDa
SequenceString: MKKYASLIFL AFLLNGCDDG DLTVDEINFD SVTPVSCTTF TENSLSTDPT IIYKLKTQEA FVLQLPQTNG LVNNNGTVTY DIDNSIYRVL YRAYNGAVAK DNICGTIPPS SPNVTEEWVG ASGKIKIVSS QVPTTTDAND SFRIEAYNHV ITFENITFQK PSGPQVQEIF ...String:
MKKYASLIFL AFLLNGCDDG DLTVDEINFD SVTPVSCTTF TENSLSTDPT IIYKLKTQEA FVLQLPQTNG LVNNNGTVTY DIDNSIYRVL YRAYNGAVAK DNICGTIPPS SPNVTEEWVG ASGKIKIVSS QVPTTTDAND SFRIEAYNHV ITFENITFQK PSGPQVQEIF EFGTFKTTVT PADLTFQNTD TGEAFNCPDN KKIYNYNASF TLTVENLDPA LLTNEATAPN QPRSQAITAT TNKVVYRNFV NGSGSITSTY DFCAAQIPSL PLLNQTWIGA DTSETKKATI EVTTEKIGDK TFIHTVVLKN VKLTKDSSYF QLGNTFTLGK ITVNL

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Macromolecule #5: LptQ

MacromoleculeName: LptQ / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 22.214863 KDa
SequenceString: MKHTLKYTFS LCFLLSMFLG YSQVVIKDTV TVRDLDDQKP KTEVAAKPSV KEIKKDSISI KTDRYGLRVG VDLYKLTRGF YDKNYKGIEF TADWRLTKKY YIAAELGFED KTTDDDRLNS TATGTYIKGG FDYNLYDNWL DMENLITIGL RGGFSSFSQD LNSYKIYNPN ...String:
MKHTLKYTFS LCFLLSMFLG YSQVVIKDTV TVRDLDDQKP KTEVAAKPSV KEIKKDSISI KTDRYGLRVG VDLYKLTRGF YDKNYKGIEF TADWRLTKKY YIAAELGFED KTTDDDRLNS TATGTYIKGG FDYNLYDNWL DMENLITIGL RGGFSSFSQD LNSYKIYNPN PYWGEQPAMS ANQKYNGLSA AWLEVALGVK AKVFNNIFVG FGVQLKLLAM NNKPSGFDNL YIPGFNRTYD GSFGVGFNYT VSYFIPIYKK KTIVPEIINQ APKK

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Macromolecule #6: LptR

MacromoleculeName: LptR / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 18.209254 KDa
SequenceString:
MKKIISLLLL FTFGLSSCEK DDICDANTPT TPRLVITFYD NAAPTSLKTV TNLKVVGEGK EDTDAIIFNE TGTSVTKYLT NANTISIPLK TDAKTTTYKF IYNATSATPN IDVLTFNYET QSVYVSRACG FKTTFTLNPR DNTANSGLIR TDPAGDGLWM LNINVVNSNI ELENETHVKV YF

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Macromolecule #7: LptT

MacromoleculeName: LptT / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 14.259058 KDa
SequenceString:
MNKIVPISLL FFLLGTVSLF AQVKEETVLV AKDSIALEEI DPLTPAKAAF YSAILPGLGQ AYNKKYWKIP LVYGAIGTSL YFYIDNNNKY RDYRNAYKRR LEGYNDDKYQ YLDESRLVAG QKFYQRNRDL SALFVVGFYV LNIIDANVDA ALIQFNVNER LSMRPEIYPN DVTFKPNVGL TFNYRF

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Macromolecule #8: LptD

MacromoleculeName: LptD / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 91.418953 KDa
SequenceString: LHTNLFNIVL ISFFLTIGCG KSYSQEIKPK KKSLPASAWS HPQFEKGGGS GGGSGGSAWS HPQFEKTSVK QTNKPATAPA AATPAVSTAT VDTIKIDSIK PKKQFLDAPT KYKAKDYAKY DKKNKLLTLY NEAELYYKDV ELKSGIIILN LEKDEVYAGR IKDSAGVLVQ ...String:
LHTNLFNIVL ISFFLTIGCG KSYSQEIKPK KKSLPASAWS HPQFEKGGGS GGGSGGSAWS HPQFEKTSVK QTNKPATAPA AATPAVSTAT VDTIKIDSIK PKKQFLDAPT KYKAKDYAKY DKKNKLLTLY NEAELYYKDV ELKSGIIILN LEKDEVYAGR IKDSAGVLVQ YPNFKQGTNE VQPDSIRFNF KTKKALIYNS RTKQGELNIK ASVTKKENDS VYFLKGARIT TAQDIDNPEY YFQTSRIKFV PGKKIVAGLT QMVIADVPTP LALPYGFFPL SKEKSVSGII IPSYNDSNTR GFSLQNGGYY FALSDNYDLT VLGDYYTNGS YAMRFESAYA KRYKYRGNIN VRFENLINSE RGYPDYSKQN IYNIQWSHSK DTKSNPNSTF SASVNMGSSK YFKRSINQAN IGSNLNNTLS SSISYNKTFN TIPGSRISLS ATHQQNTQTE EILMTLPNFQ GSIDRIYPFV GENGVKKGFF KNINLQYNVT GKNNFKTTDS LFFKPQMFRD AQIGMQHSIP ISTNFKIFKY FSAGASTNYQ ETWVTKTIDK NYDASKGQVA STTVNGFDAF RTYNFSTNLG TTIYGTFNFG TDKKIQSIRH VMRPSITYSY TPSFERYYDH YTVDAAGRIS TDEYTRFENG IYGAPGKENS NIVGFSLSNT FEAKVRDSDS TKTEPKKIML LNNLNFSTSY NFNANGKETL AWQPIIVSGG TQFFENKMNV NFGAVLNPYA IDNAGNVINM YNIENGGSLF RMTSANITMN YSFSNKGTGK EKNTQSQRNG GRNDDLFGTN TDLNDSRNSQ FANDPDREED VITEFFSSKL PWDMTMAYSL TYSNANRENK ITGNSIMISA NMDITPKWKG GVSTGFDFVQ KGVTFTQFRF ERDLLSWRMA FNWQPMGTSS NWNFFIGIKS GMLSDIKWNK RSTINR

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Macromolecule #9: LptE

MacromoleculeName: LptE / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 16.972932 KDa
SequenceString:
MKHLKYLLLL LVATTFSGCG VYNFTGASPI DAKTFQVSFF HNNADLVEPG IDRDFTLALQ DLIMNQTNLN LVSNGGELAY EGEIVDYRIT PMTATAVTST GDVGAAQNRL TIRINVRFTN KKKETDDFEK PFEFYYDFPG ASLPTGSVLN EAIKTIFERI TQDIFNESLA KW

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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 correctionSoftware - Name: SIMPLE / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 218874
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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