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- EMDB-16793: Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S... -

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Basic information

Entry
Database: EMDB / ID: EMD-16793
TitlePhotorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S, C20S, C870S, T1279C mutant
Map dataLocal resolution filtered map that was used for model building
Sample
  • Complex: TcdA1
    • Protein or peptide: TcdA1
KeywordsBacterial toxin / Tc toxin / TOXIN
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
ABC toxin, N-terminal domain / ABC toxin N-terminal region / TcA receptor binding domain / TcA receptor binding domain / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain
Similarity search - Domain/homology
Biological speciesPhotorhabdus luminescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsNganga PN / Roderer D / Belyy A / Prumbaum D / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: to be published
Title: Kinetics of the syringe-like injection mechanism of Tc toxins
Authors: Nganga PN / Folz J / Kucher S / Roderer D / Xu Y / Sitsel O / Belyy A / Prumbaum D / Assafa TE / Kuehnemuth R / Dong M / Seidel C / Bordignon E / Raunser S
History
DepositionMar 3, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16793.png

Downloads & links

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Map

FileDownload / File: emd_16793.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map that was used for model building
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.062701255 - 0.13488755
Average (Standard dev.)0.00044529518 (±0.0048162187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 337.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16793_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_16793_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A map that was used to model the...

Fileemd_16793_additional_1.map
AnnotationA map that was used to model the receptor binding region in the open state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map

Fileemd_16793_half_map_1.map
AnnotationSecond half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First half map

Fileemd_16793_half_map_2.map
AnnotationFirst half 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 : TcdA1

EntireName: TcdA1
Components
  • Complex: TcdA1
    • Protein or peptide: TcdA1

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Supramolecule #1: TcdA1

SupramoleculeName: TcdA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 1.5 MDa

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Macromolecule #1: TcdA1

MacromoleculeName: TcdA1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 285.329625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHSS GLEVLFQGPM NESVKEIPDV LKSQSGFNSL TDISHSSFNE FRQQVSEHLS WSETHDLYHD AQQAQKDNRL YEARILKRA NPQLQNAVHL AILAPNAELI GYNNQFSGRA SQYVAPGTVS SMFSPAAYLT ELYREARNLH ASDSVYYLDT R RPDLKSMA ...String:
MAHHHHHHSS GLEVLFQGPM NESVKEIPDV LKSQSGFNSL TDISHSSFNE FRQQVSEHLS WSETHDLYHD AQQAQKDNRL YEARILKRA NPQLQNAVHL AILAPNAELI GYNNQFSGRA SQYVAPGTVS SMFSPAAYLT ELYREARNLH ASDSVYYLDT R RPDLKSMA LSQQNMDIEL STLSLSNELL LESIKTESKL ENYTKVMEML STFRPSGATP YHDAYENVRE VIQLQDPGLE QL NASPAIA GLMHQASLLG INASISPELF NILTEEITEG NAEELYKKNF GNIEPASLAM PEYLKRYYNL SDEELSQFIG KAS NFGQQE YSNNQLITPV VNSSDGTVKV YRITREYTTN AYQMDVELFP FGGENYRLDY KFKNFYNASY LSIKLNDKRE LVRT EGAPQ VNIEYSANIT LNTADISQPF EIGLTRVLPS GSWAYAAAKF TVEEYNQYSF LLKLNKAIRL SRATELSPTI LEGIV RSVN LQLDINTDVL GKVFLTKYYM QRYAIHAETA LILCNAPISQ RSYDNQPSQF DRLFNTPLLN GQYFSTGDEE IDLNSG STG DWRKTILKRA FNIDDVSLFR LLKITDHDNK DGKIKNNLKN LSNLYIGKLL ADIHQLTIDE LDLLLIAVGE GKTNLSA IS DKQLATLIRK LNTITSWLHT QKWSVFQLFI MTSTSYNKTL TPEIKNLLDT VYHGLQGFDK DKADLLHVMA PYIAATLQ L SSENVAHSVL LWADKLQPGD GAMTAEKFWD WLNTKYTPGS SEAVETQEHI VQYCQALAQL EMVYHSTGIN ENAFRLFVT KPEMFGAATG AAPAHDALSL IMLTRFADWV NALGEKASSV LAAFEANSLT AEQLADAMNL DANLLLQASI QAQNHQHLPP VTPENAFSS WTSINTILQW VNVAQQLNVA PQGVSALVGL DYIQSMKETP TYAQWENAAG VLTAGLNSQQ ANTLHAFLDE S RSAALSTY YIRQVAKAAA AIKSRDDLYQ YLLIDNQVSA AIKTTRIAEA IASIQLYVNR ALENVEENAN SGVISRQFFI DW DKYNKRY STWAGVSQLV YYPENYIDPT MRIGQTKMMD ALLQSVSQSQ LNADTVEDAF MSYLTSFEQV ANLKVISAYH DNI NNDQGL TYFIGLSETD AGEYYWRSVD HSKFNDGKFA ANAWSEWHKI DCPINPYKST IRPVIYKSRL YLLWLEQKEI TKQT GNSKD GYQTETDYRY ELKLAHIRYD GTWNTPITFD VNKKISELKL EKNRAPGLYC AGYQGEDTLL VMFYNQQDTL DSYKN ASMQ GLYIFADMAS KDMCPEQSNV YRDNSYQQFD TNNVRRVNNR YAEDYEIPSS VSSRKDYGWG DYYLSMVYNG DIPTIN YKA ASSDLKIYIS PKLRIIHNGY EGQKRNQCNL MNKYGKLGDK FIVYTSLGVN PNNSSNKLMF YPVYQYSGNT SGLNQGR LL FHRDTTYPSK VEAWIPGAKR SLTNQNAAIG DDYATDSLNK PDDLKQYIFM TDSKGTATDV SGPVEINTAI SPAKVQII V KAGGKEQTFT ADKDVSIQPS PSFDEMNYQF NALEIDGSGL NFINNSASID VTFTAFAEDG RKLGYESFSI PVTLKVSTD NALTLHHNEN GAQYMQWQSY RTRLNTLFAR QLVARATTGI DTILSMETQN IQEPQLGKGF YATFVIPPYN LSTHGDERWF KLYIKHVVD NNSHIIYSGQ LTDTNINITL FIPLDDVPLN QDYHAKVYMT FKKSPSDGTW WGPHFVRDDK GIVTINPKSI L THFESVNV LNNISSEPMD FSGANSLYFW ELFYYTPMLV AQRLLHEQNF DEANRWLKYV WSPSGYIVHG QIQNYQWNVR PL LEDTSWN SDPLDSVDPD AVAQHDPMHY KVSTFMRTLD LLIARGDHAY RQLERDTLNE AKMWYMQALH LLGDKPYLPL STT WSDPRL DRAADITTQN AHDSAIVALR QNIPTPAPLS LRSANTLTDL FLPQINEVMM NYWQTLAQRV YNLRHNLSID GQPL YLPIY ATPADPKALL SAAVATSQGG GKLPESFMSL WRFPHMLENA RGMVSQLTQF GSTLQNIIER QDAEALNALL QNQAA ELIL TNLSIQDKTI EELDAEKTVL EKSKAGAQSR FDSYGKLYDE NINAGENQAM TLRASAAGLT TAVQASRLAG AAADLV PNI FGFAGGGSRW GAIAEATGYV MEFSANVMNT EADKISQSET YRRRRQEWEI QRNNAEAELK QIDAQLKSLA VRREAAV LQ KTSLKTQQEQ TQSQLAFLQR KFSNQALYNW LRGRLAAIYF QFYDLAVARC LMAEQAYRWE LNDDSARFIK PGAWQGTY A GLLAGETLML SLAQMEDAHL KRDKRALEVE RTVSLAEVYA GLPKDNGPFS LAQEIDKLVS QGSGSAGSGN NNLAFGAGT DTKTSLQASV SFADLKIRED YPASLGKIRR IKQISVTLPA LLGPYQDVQA ILSYGDKAGL ANGCEALAVS HGMNDSGQFQ LDFNDGKFL PFEGIAIDQG TLTLSFPNAS MPEKGKQATM LKTLNDIILH IRYTIK

UniProtKB: TcdA1

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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: 11.2
Component:
ConcentrationFormulaName
100.0 mMC9H19NO3SCAPS
150.0 mMNaClSodium Chloride
0.1 %Tween-20
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 13059 / Average electron dose: 78.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 573814
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rw6

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 80710
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8cq2:
Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S, C20S, C870S, T1279C mutant

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