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- EMDB-50537: CryoEM structure of the neck (1403-2314) in the grappling hook pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-50537
TitleCryoEM structure of the neck (1403-2314) in the grappling hook protein A (GhpA) in the bacterium Aureispira sp. CCB-QB1
Map data
Sample
  • Complex: Crude purification of the grappling hooks from the surface of the bacterium Aureispira sp. CCB-QB1.
    • Protein or peptide: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1
Keywordsixotrophy / type 9 secretion system / cryoEM / surface protein / predation / CELL ADHESION
Biological speciesAureispira sp. CCB-QB1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLien Y-W / Amendola D / Lee KS / Bartlau N / Xu J / Furusawa G / Polz MF / Stocker R / Weiss GL / Pilhofer M
Funding support Switzerland, European Union, United States, 6 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_212592 Switzerland
European Research Council (ERC)679209European Union
European Research Council (ERC)101000232European Union
Swiss National Science Foundation315230_176189 Switzerland
Simons Foundation572792 United States
Simons Foundation542395 United States
Citation
Journal: Science / Year: 2024
Title: Mechanism of bacterial predation via ixotrophy.
Authors: Yun-Wei Lien / Davide Amendola / Kang Soo Lee / Nina Bartlau / Jingwei Xu / Go Furusawa / Martin F Polz / Roman Stocker / Gregor L Weiss / Martin Pilhofer /
Abstract: Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be ...Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.
#1: Journal: Biorxiv / Year: 2024
Title: Mechanism of bacterial predation via ixotrophy
Authors: Lien YW / Amendola D / Lee KS / Bartlau N / Xu J / Furusawa G / Polz MF / Stocker R / Weiss GL / Pilhofer M
History
DepositionJun 5, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50537.png

Downloads & links

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Map

FileDownload / File: emd_50537.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 540 pix.
= 920.16 Å		1.7 Å/pix.
x 540 pix.
= 920.16 Å		1.7 Å/pix.
x 540 pix.
= 920.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.704 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-1.9141985 - 4.9377365
Average (Standard dev.)-0.0013473845 (±0.09691041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 920.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50537_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_50537_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_50537_half_map_2.map
Projections & Slices
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Sample components

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Entire : Crude purification of the grappling hooks from the surface of the...

EntireName: Crude purification of the grappling hooks from the surface of the bacterium Aureispira sp. CCB-QB1.
Components
  • Complex: Crude purification of the grappling hooks from the surface of the bacterium Aureispira sp. CCB-QB1.
    • Protein or peptide: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1

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Supramolecule #1: Crude purification of the grappling hooks from the surface of the...

SupramoleculeName: Crude purification of the grappling hooks from the surface of the bacterium Aureispira sp. CCB-QB1.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aureispira sp. CCB-QB1 (bacteria)

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Macromolecule #1: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1

MacromoleculeName: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1
type: protein_or_peptide / ID: 1
Details: The structure of Neck covers the amino acid residues from 1403 to 2314 in GhpA.
Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Aureispira sp. CCB-QB1 (bacteria)
Molecular weightTheoretical: 610.114375 KDa
SequenceString: MQIQRHSFKW ILYGFLCWMT SFVQAQTPTL TNATPAEGFI GEQVCFPVTF VNTGAPGYGP YVRLIVPTGF TFDNASFGGS IQTVQNLGV IVSGAPNNFV IDPIAQSNNN STTSDTIFAP VGSTVILLEY PVGSMVQGGV SLISEVCMTV DPAATIGVPV D ICTQGVYE ...String:
MQIQRHSFKW ILYGFLCWMT SFVQAQTPTL TNATPAEGFI GEQVCFPVTF VNTGAPGYGP YVRLIVPTGF TFDNASFGGS IQTVQNLGV IVSGAPNNFV IDPIAQSNNN STTSDTIFAP VGSTVILLEY PVGSMVQGGV SLISEVCMTV DPAATIGVPV D ICTQGVYE FGDTPTGDNG PIAGANECEP IIPILFRFDK KVNGSDGVYN EVPGGGASLC HIHQYELNID IAAAGTLNGP IT ITDVLPG ELAYFGNISL PAGCSAVEPT VGGLGGTLTV TCNGSYPGST ANIDMQVTFD AAVSDTLDET ICDDTDINNG ATV NVPGNP SQSDTVVTHV EHVLLGHTNN TVSPVTIGQT VLYTIGAEIT EYTAGLTAAS ITFIVPDGMI YNPASLTWAG TPVA AGNVV IVPGPGTGST VTVDVHTQNG ANILPCASPS LQYTADVNQT YANGDPVLSR DRLTHSSTLT YDLVEGATGC TTSAG TPID VIDIFFQKTV NNSPPTGPGR NGQWWPGDVV QYRLELQIPS LDLDDVVITD FFPLPIHDVA SLAATFGTDV RFDPAT CWN TAPVTYTRDI PTNSLILDFG DVSDLVTGGC VDIVLLIDIP ITTLPFADGL FHSNFMQVNS DNSTADNITN SALTLIQ VG APDLELTKGI VSSDNPNVTI SPTVVPPDGN ATDVSAGDQL FFDITIENVG GAPGYDVQVR DVAPPELTNC ALVAPNPV V DGSNNALAFS GGFVGNTLTI DLVAPNDSIA FATAPNNNDL ITVSYVCEAV AGIQAGTRFD NTAEVDWSST RGGVKFPPV EDDANGRIAD PTMNKVVDYI FPNYSNTNTQ ASIGEVVAYE LQLNIPEGNM NNVTLVDQVD EGLAFVAVDS IVICNSSGST NIITSIGGG FPAVQSGATI TNLGANPQQQ DRVLTLDFGN LQNLDTDNIE DTIKVYYRTI VINHVTNFDG ERVRNRAVLS W DNPNTPGD RSSINDRAPF VTIVEPQLEI SKSFTPDEVL PGNNSFVTLT VRNPGTSSAP AFDVSLTDIL PTGMTFVSGF SA GGTASIT TPPTNGGGTI TAHWDTINVG EVYSITFEVQ ASSSITPCFT LTNCANLVWE SIAEADEPNM PTAFSSNLGV QRT GNPGNL GGAANTYTQD SCADLDVVID NTFDPFITAN TPLCEGDRVV LTVQQYQGNV VRYNWTGPGV PAGFNNYELV LDPV TTADT GTYFVYVELD GCITDTSNFF SLQLRPKPVT PNINPGDTTI CEGTSIQFST STIANDYTWT GPNGFTANSA TTPLI SPVT LADAGRYTLF TTNAQGCNSD PISSNLTVTP RPAQPSIASN TPICSNENII LTSSTSAITY QWMAPNGQDT ITTNNT LTL EPNNPLYTAG NWTLVVFDAN GCASQPSTAA NVIINGTPIA PMTSNSGPIC EGEDVTLMVN TVSSGTYAWY SDANLTN LV ASTQNPVISG LLASNSPDTF YVQVSSNGCL SDTGFTVVQV NPNPAAVSPG YTPLCSGDTI FLFANATANI YNWTGPNG F VSNLENPFIA NSAALNAGSY TVSITDANGC SNSGIVQVAV DERPVTPTIT GNGPVCEGDN IQLNIGSYTG TTVQYTWST PTGVVTTGVP SLNINNTTVA DSGLYSVVVA VDGCTSLADS INIVVRPNPI APNVPSNFSV CEGDGIALTT TTNANIYNWT GPNGFSSNS PNPTVISPAS SANAGTYTLV VQDFNGCTSP AASTVVTVNA APAQPSMTTN SPICNGADLV MSTSAAGNSY I WRAPNGAD TTTASSTLTI VPTSSLYQSG NWTLSVVNAA GCVSPASIAS AVEINSIPST ASAGNNGPVC TGTDASLSAG TV SGASYAW YTDAGTSNQF STLQNPTVNN LTNDSTFYLL VTVNGCPSAL DSTTVVVYPL TPSPSLPANF AVCEGDDIAL STS TVASSY DWSGPNGFTS NAQNPVVITN ATGSNAGVYT LSIVDGNGCS SADTSVQVTV NAAPTQPSMT TNSPICNGAD LVMS TSAVG NSYIWRAPNG ADTTTASSTL TIVPTSSLYQ SGNWTLSVVN AAGCVSPASI ASAVEINSIP STASAGNNGP VCTGT DASL SAGTVSGASY AWYTDAGTSN QFSTLQNPTV NNLTNDSTFY LLVTVNGCPS ALDSTTVVVY PLTPSPSLPA DFAVCE GDD IALSTSTVAS SYDWSGPNGF TSNAQNPVVI TNATGSNAGV YTLSIVDGNG CSSADTSVQV TVNAAPAQPS MTTNSPI CN GADLVMSTSA TGNSYIWRAP NGADTTTASS TLTIVPTSSL YQSGNWTLSV VNAAGCVSPA SIASAVEINS IPSTASAG N NGPVCTGTDA SLSAGTVSGA SYAWYTDAGT SNQFSTLQNP TVNNLTNDST FYLLVTVNGC PSALDSTTVV VYPLTPSPS LPADFAVCEG DDIALSTSTV ASSYDWSGPN GFTSNAQNPV VITNATGSNA GVYTLSIVDG NGCSSADTSV QVTVNAAPTQ PSMTTNSPI CNGADLVMST SAVGNSYIWR APNGADTTTA SSTLTIAPTS SLYQSGNWTL SVVNAAGCVS PASVASMVTI N NGTNPTAF NNGPVCRGDA VQLNTTTINN ALYEWYSDAA LTNLISTQQN PTVANITTDS TFYLVVTVNG CPSSAVATTV TL HPTPATP NIPANFVVCE GETIALSTST VASSYNWTGP NGFTSNLQNP AVIQPATTAD AGSYTLFIVD ANGCQSADTS VVV GVNRGP AAPVLTNNSA ICDGDTLLLS TTASADTFRW ISPNGIDTIT TVNSLMIVPT NGTYYQSGDW TLITQVANNC PSEP SAPSS VVINSSTAAP TAFNDGPVCV GGDVTLSTPS APGAFYQWYT DAALTNLVAT TASFTAINIT QDSTFYLVVT VNGCT SPAG STVVNVIGQP SAPNVPADFE VCEGDDIILG TTTIAASYSW TGPNGFTSNL QNPAAITNAS LIDSGIYRLV VTYSNG CVS ADTTVRVGVN SNPPVPNIVS NGPICFGDTL VLSSSTSCGQ SQWIGPNGNS QSTLGTPGGS NVLWTIGSTT SIPMNNA NY LPGNWYMICI DTVTGCRSES NTINVIINAN PDTPAVFNDG PVCEGGNSNL STATVSGASY AWYSDSSLTS LVSTAQNP M IVNISTDTTW YLVVTVNGCS SVAGSTTVIV HPTPVTPNVP ANFAVCEGDN ITLSTSTVAS SYNWSGPNGF TSNVQNPVV ITNATTSNAG VYTLSIIDGN GCESGDTAVT VTVDSIPATP VLSSNSAICF GDTLELSTTA LATSYEWIAP DGSRITTGTN ILSISSNNS LYQSGDWMLV TTNASGCTSM PSSVATVVIN ANPAQPAVFN DGPVCEGGNS NLSTATVSGA SYAWYSDSSL T SLVSTAQN PMIVNISTDT TWYLVVTVNG CSSVAGSTTV IVHPTPATPN VPANFAVCEG DNITLSTSTV ASSYNWSGPN GF TSNVQNP VVITNATTSN AGVYTLSIVD GNGCESGDTT VTVTVDSIPV TPVLSSNSAI CFGDTLELST TALATSYEWI APD GSRITT GTNILSISSN NSLYQSGDWM LVTTNASGCT SMPSSVATVV INANPAQPAV FNDGPVCEGG NSNLSTATVS GASY AWYSD SSLTSLVSTA QNPMIVNIST DTTWYLVVTV NGCSSVAGST TVIVYPTPAT PNVPANFAVC EGDNITLSTS TVASG YNWS GPNGFTSNVQ NPVVITNATA SNAGVYTLSI VDGNGCESGD TTVTVTVNGN PPVATITSNS PICFGDTLTL SSSTNC GQS QWIGPNGNSS GTLGTPGGNN VLWTIGSTTN IPSTDVNYLS GDWYMICIDT ITGCRSESNT ITIEINPIPV VSAFNNG PI CAGEDGELSA TFITGASYRW YSDATLTTLI STSRTPIISS MMSSETYYVV ATVNGCTSLA DSTTIVVNPT PVIPNPTY T PLCQLDTLFL QANAVGPIAT YWWTGPNGFT SHLENPVIPN IYPFNAGSYI LTVTDSLGCE AVSTVEVTIY PKPQTPTIA HNAPFCEGTN DLTLTTQAYF GTDVRYIWTL PNGNLDTTFV PSLVLPNATV QDTGAYSLVV WIDGCLSLPA EEIIRIYPTP ATPNVPADF AVCEGEAIVL TTTTNATSYF WTGPNGFQSN LQSPSVVNAT LVDAGSYHLY VTNTWGCQSL DTSVQVTVNA N PPIATITS NSPICFGDTL TLSSSTNCGQ SQWIGPNGNS TGTLGTPGGN NVLWTIGSTT NIPSTDSNYL SGDWYMICID TI TGCRSES NTITIDINPI PSTPAAFNNG PICIGGTAQL STTTVSGATY AWYADATLTT LVATNQNPTI SNITTDSTFY IVV TVNGCS SLAGSTTVST YPVPATPAVP ADFAVCEGDN IVLSTTTVAA GYNWTGPNGF TSNLQNPSVV SASLVDSGTY TLFI IDANG CPSGDTSVQV SVHPNPVQPV LSSNSAICDG DSLVLSTTAT ATTYRWVAPD GADTLTTVNT LVILPSNAFY QDGNW TLMT MDANGCQSIL SNPESVTIHS IPAAQAVFNN GPVCRGSSVN LSTSFISGAT YEWYADAALT ILVATSQNPT INNITT DST FYLVITVNGC TSAAGATTVV VHPTPTTPNV PSNITVCEGD AIVLTTTTNA SAYVWSGPNG FSSNQQSPTV INAATVV DS GKYSLYVIDA NGCRSEDTSL QVVVNPTPTT PLIVSNNTPI CEGSNIVLSA NAGAAGTTYE WFNASNVSVG TGQTLTIV G ATVADAGDYY VITTLNSCSS AASSTTTAIV DQVPSTAAFA GNDINLCNSF TTTLDATPPN SATGFWTTNS GATIANPNL ANSAVYNLPT GTSTFYWTLS NGACIDFSVD SMVVEVTPAS TDVADAGLDQ NLCGQTSATL TAANPSTATG QWTQSASQAG QGIVITNPT NPNTTVTGLQ QGNNYTFTWT LSNGNCTDYS TDMVQINVDV SPPDNAYAGV DILLCNQNTA NLDAFVSQYG T GMWTSTSS ATIIDPTLAN TTVINLPQDT SVFVWTLSNG TCQNYSTDSV LVVVSTTTDT AEAGNNQVVC SVNALTLGAT MP SSGFGTW SQTAAQAAQG VVIVDVNDPN TQVVGLNAGT TYAFTWTLSN GTCQDYSSDV TTISVNATPP DNAFAGNDIN LCG VATTTN LAASVPTVAM GLWTTTSSAT ISNPTQPNST VSGLSAGQNI FIWTLSNGTC QDYDSDTVIV TVTTPSSDVA DAGL DSAYC AQSVVTLNAV APSVGGGYWS QTPSQASLGA VIDNPTDTAT TVSNLMPGVT YTFTWTLTNG GCVDYSSDQV LITID VLPT NVAYAGEDTI LCGGNAVQLD GLAPPIGTGF WTTNDTATIV TPVDPNSLVV NIAEDTTTYY WTLSNGACVD YSVDSV TVI ISPASTDLAF AGYDEVLCGV DSIMLSAAVP TTSTGIWTQS AGQASQGIVI TNPTNPNSSV TGIQAGQVYT FTWTLST FG CANFSTDDVQ YTINALPPEV AYAGPDIVLC TGNSVTMDAN NPIFSTGVWS SNSSAVIVNP TLSNSNIVNI PTDTVAFY W SLSNGSCADY SIDTMLIIVT PTFSVDTANA GLDINLCNED TAQLMAIAPN VATGRWTQPF NQSSAGVVIT DPNAAMTTA TGLQLDSTYT FTWSVSNGPC RDYDRDQVIV QVSTLPTDAA YAGEDFVICG IDTAIVSATA PSIGAGMWTT TTTATIVTPP STRTELLNL SLGSNEFIWT LSNGACRDYS SDTIVITMDS APIANADSFV VIYNSNGNTI DVTPNDGLNN NWVITISESI A SGTLDNLG TGEFDLFLQD VLVDQRFIYQ LCNPNCPAIY CDTALVTIDV QGGTECNFPN MITPNNDDAN ETFIVPCLDG LE GTKFAVY NRWGDLMYEN DNYKNDWGGT HNGVPVPDAT YFYIMELADG QRFQGFVEVR R

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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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Details: a featureless cylinder with a diameter of 9 nm as reference
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12450
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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