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- EMDB-44168: Pseudomonas phage Pa193 baseplate complex and tail fiber -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44168
TitlePseudomonas phage Pa193 baseplate complex and tail fiber
Map data
Sample
  • Virus: Pseudomonas virus Pa193
    • Protein or peptide: x 11 types
Keywordsphage / bacteriophage / baseplate complex / STRUCTURAL PROTEIN / VIRAL PROTEIN / tail fiber
Function / homology
Function and homology information


lytic transglycosylase activity / peptidoglycan metabolic process / membrane
Similarity search - Function
Baseplate hub gp41 / Baseplate component gp38 / Protein of unknown function DUF2612 / Protein of unknown function (DUF2612) / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Tail fiber protein gp32 / Baseplate protein J-like / Baseplate J-like protein / Vgr protein, OB-fold domain superfamily ...Baseplate hub gp41 / Baseplate component gp38 / Protein of unknown function DUF2612 / Protein of unknown function (DUF2612) / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Tail fiber protein gp32 / Baseplate protein J-like / Baseplate J-like protein / Vgr protein, OB-fold domain superfamily / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Phage protein / Tail fiber protein / Tail fiber protein / Phage protein / Baseplate protein J-like domain-containing protein / Phage protein / Internal (Core) protein / Tail fiber protein / Phage protein / Baseplate protein
Similarity search - Component
Biological speciesPseudomonas virus Pa193
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsIglesias SM / Cingolani G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM140733 United States
CitationJournal: Commun Biol / Year: 2024
Title: Cryo-EM analysis of Pseudomonas phage Pa193 structural components.
Authors: Stephano M Iglesias / Chun-Feng David Hou / Johnny Reid / Evan Schauer / Renae Geier / Angela Soriaga / Lucy Sim / Lucy Gao / Julian Whitelegge / Pierre Kyme / Deborah Birx / Sebastien Lemire / Gino Cingolani /
Abstract: The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various ...The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold vertex. We also visualized a large portion of Pa193 ~ 500 Å long tail fibers and resolved the interface between the baseplate and tail fibers. The work presented here provides a framework to support a better understanding of phages as biomedicines for phage therapy and inform engineering opportunities.
History
DepositionMar 20, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44168.png

Downloads & links

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Map

FileDownload / File: emd_44168.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.34 Å/pix.
x 480 pix.
= 643.2 Å		1.34 Å/pix.
x 480 pix.
= 643.2 Å		1.34 Å/pix.
x 480 pix.
= 643.2 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-13.446484 - 34.242905
Average (Standard dev.)-0.000000000002658 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 643.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44168_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_44168_additional_1.map
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Half map: #2

Fileemd_44168_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_44168_half_map_2.map
Projections & Slices
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Sample components

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Entire : Pseudomonas virus Pa193

EntireName: Pseudomonas virus Pa193
Components
  • Virus: Pseudomonas virus Pa193
    • Protein or peptide: gp45-a Baseplate wedge 1
    • Protein or peptide: gp47 Tail fiber
    • Protein or peptide: gp34 helical bundle
    • Protein or peptide: gp38 Ripcord-1
    • Protein or peptide: gp41 Tape measure protein
    • Protein or peptide: gp42 Tail hub
    • Protein or peptide: gp39 Ripcord-2
    • Protein or peptide: gp46 Baseplate wedge 2
    • Protein or peptide: gp37 Baseplate tube
    • Protein or peptide: gp35 Sheath initiator
    • Protein or peptide: gp44 Tail tip

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Supramolecule #1: Pseudomonas virus Pa193

SupramoleculeName: Pseudomonas virus Pa193 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2590837 / Sci species name: Pseudomonas virus Pa193 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: gp45-a Baseplate wedge 1

MacromoleculeName: gp45-a Baseplate wedge 1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 43.189418 KDa
SequenceString: MANYNYIVDT GVIVADTADV LSDVEAEFRA ALGANINLAA STPQGSLVAA EAIARSSVMR NEARIANTIN PNVSFGTFLD AICALMGIE RGSDLSTFGY GVQVTGRSQT RISTGSRVQT PAGAIFTVLS DVTIPAGGVA TIDIKSQEYG NIPLPVGNLI I IDGTIGWS ...String:
MANYNYIVDT GVIVADTADV LSDVEAEFRA ALGANINLAA STPQGSLVAA EAIARSSVMR NEARIANTIN PNVSFGTFLD AICALMGIE RGSDLSTFGY GVQVTGRSQT RISTGSRVQT PAGAIFTVLS DVTIPAGGVA TIDIKSQEYG NIPLPVGNLI I IDGTIGWS GAKVIASTRV DPGSRQMSDA ELKNARVNRL AIQGRNSTMA IKAYVSAVPN VTSVNVIENN TGAVQVVNGV SF TLPYAVW VCVAGNPDKQ AVADALWAAH NGGTPWDYGA TNNGVPVDGP NGVPVRDPAS GRKYVVKWTT PIMYDGYVNV TVQ QGSSSV APEAIQNAVV NYAQGKVEGE EGLVVGASLS AFEVAGAIAR EIPGIYIKLC QVACVAAGSP APAPGDFTSE YVMS AFGQA TISVGNVRVT FV

UniProtKB: Baseplate protein J-like domain-containing protein

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Macromolecule #2: gp47 Tail fiber

MacromoleculeName: gp47 Tail fiber / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 103.353273 KDa
SequenceString: MITPELIPSP FAAQGDKDPI PQTSSTGFAN LRDGYTPDYE ISLASNNPQA KAVERKIQNQ LFFIATQNAQ AWQRQMAPPW FQGMPGGYE QNAEVVRVGN DGIMRRYRSM VNANASDPLS STTWEEQPAW SAMRSNIPMP AGGPGLSSGG EVITTGRNFN D LLNGTWEF ...String:
MITPELIPSP FAAQGDKDPI PQTSSTGFAN LRDGYTPDYE ISLASNNPQA KAVERKIQNQ LFFIATQNAQ AWQRQMAPPW FQGMPGGYE QNAEVVRVGN DGIMRRYRSM VNANASDPLS STTWEEQPAW SAMRSNIPMP AGGPGLSSGG EVITTGRNFN D LLNGTWEF FSDSVVIASQ NAPVYPASAG AAAGMLEAKS WISGSNTFCV QRYTDRVGNV AVRGLNAGAW TNWMYAVNVM AL QQGRVTY GVAAGPANAY TLTLVPQLQG GLVDGMILRV KFNTMNTGAS TINVSGLGAK AIVGAANFPL TGGELGQGLI AEL VFDAAG DRWRILAGAP RIQVGNADQD YQAPSWKQVK DYVASQKLTE VDWADVVNKP NVAIQDTTPW FANLELSDAR PFID FHFNN NRAKDFDYRF ISEADGSMAF YSRQGSAGPT QDILFSRSNV TFLQPRLDVA KNLAYIANSG PLWQNTTADQ PGWKF TFAQ GVDANNNAVI AVNTTNPDGS YRSQIMRWDW ASTNVIFNNR PLFAGQYVPW DSGNFDPSTK LTVNATNQIA GPTGIR NTN GNTGNMNTWG SGSTTASYGN AAIQIFGKGG GEPAAIYFDN SQTGWYLGMD KDGQLKRAGW SLGNNSYVIT DELNIRN HI NGMAARPVWG GNEFWGPWNF NPNTKLTLGA FNDSQHTRMV NSAAKDVGIA AMTSYGDAAM SFFNYEASTP TGNRAAVI S FVRNGARGVL FGLDTDNKLK WGGYSLGAVA FEIADSNNLM SLWSSHAAAP NWNGQTIWRS GNFNPDTKAT LAARNTTSS PTIFSYGASG IASTGQVGAL VVENNSVTNT AAAITFHSPQ KYQVNFGLDA DNVVKIGGGT MGGVAYPIIH SGNYNNYINQ ALVQVGLGG VGSYAILAVF DTSAPAASIA PGTIMDSSKL FYSSCDSTYR SSASPTGTWR CMGYVYNRDS TNGDSASLFQ R VT

UniProtKB: Tail fiber protein

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Macromolecule #3: gp34 helical bundle

MacromoleculeName: gp34 helical bundle / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 12.270898 KDa
SequenceString:
MKKIPLTAVP NQAISFNAGS SYWKIRLYQN MDMMNADISR DGVIVCHGVR CFGGIPLLQY SRQYRPDYGN FVFDRDADWT LFGDGINLF YLDGAEFAEY QALATRKE

UniProtKB: Phage protein

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Macromolecule #4: gp38 Ripcord-1

MacromoleculeName: gp38 Ripcord-1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 20.000949 KDa
SequenceString:
MMLGIFTSLL SSRSFSIVDQ NTNQLVAADL RISRVNTRFS SVGQRHMLED GKTKMDSRTI HPMEIIVEVF CPSIDVVDQI NQLLLDRDT LYKVITRGMV FERMMCTSEA LNQTPDMISA TPARLTFSQV LVQNPKPIMF RNAGDSSMID RGLALAEDVV G SAGDLFDY AVNGVQNAAD LF

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Macromolecule #5: gp41 Tape measure protein

MacromoleculeName: gp41 Tape measure protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 94.380547 KDa
SequenceString: MSSDLDEFIL RYEADTARAE RNLEHLQNQI RRVNSASTSG LQDLRHFADG AATELGRVVP QIDSVTSAIR GMNAQLAIGA TGVALVAAG VKAFMNTRDQ YNQQRIQAMD IGIAPARLEE YQRKFVRQSG GTISREQGAE MTKNLADTFR RAYRDIGRVG P EARILRMA ...String:
MSSDLDEFIL RYEADTARAE RNLEHLQNQI RRVNSASTSG LQDLRHFADG AATELGRVVP QIDSVTSAIR GMNAQLAIGA TGVALVAAG VKAFMNTRDQ YNQQRIQAMD IGIAPARLEE YQRKFVRQSG GTISREQGAE MTKNLADTFR RAYRDIGRVG P EARILRMA GVDVGSFQKG MRPLNDIITD LATKMAKLKP DEISAYADAL GVSRDYLSTL AKIGPAMGKV TEMTTAELQS RV QGESNIQ KFNDALANLN QTFTTLENRV GEKLAPAFTK LIEIIDKIVQ AIPNEVESFA KDTKSRWEDG VLGKATVGSD ILS LLSPGA LLGRLAAWGT RRGMEESGLI DKDKVPGAQT SEDLAKKQED QDKATKSMKE LEKLADQTTK STNDFAVAIN MFSG AVSSF ANAVDERQAW AAWAGEIGRA VGMGSTAPTS RATGVYPHAI YDQSKSGAAG QVFGEPIGAQ SLRNRMFSPQ RKAEP VTVP SYINDIIKDA SKMYNIPELD IKKLIYTESR FNARATSEAG AKGLMQLMPE IAKAYGITDV YDPRQNILGG TRLLRE NLD RANGDMRLAL TYYHGGLDPK NWGPRTRAYP GLVMSAPIEL MEEAQRKQKA AAMTVANETF APEGGDMDIR PYDGGRL ET PDQGKKEDER REARRYDDRV VRPEIRIIDR MPDRSDGEIL KMSRRQEADR ADSGFRKFPN QVRGETKQNI QAQLTAGA I AQVIGVNPNQ IMRREISRSD LLFGYNQAIL GKQQEIKAAA TEANNVFLSP AKLAEATAKV NAASREMDIL RTYGEQLLK SAPERGQELT IGRIDMLVNV TGANSPEEAR EIFSKQTADQ LTTAIQDAQN DSATKILY

UniProtKB: Internal (Core) protein

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Macromolecule #6: gp42 Tail hub

MacromoleculeName: gp42 Tail hub / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 32.480277 KDa
SequenceString: MKKRILRVTF NMPYGPEVIR EDLDVRVRIM KAALRIQNRA TMEIFGLTTQ LRESLLSQFT AWKHRQRQVG REDELMIKVS VEAGYSDQG REQVSRVFVG EVAIVDIISP PPDIGIRIQC YTRQIDRTKT IRNMPPANTT FVKFVEWGAN EMGLNFICDT S YNDQVLKN ...String:
MKKRILRVTF NMPYGPEVIR EDLDVRVRIM KAALRIQNRA TMEIFGLTTQ LRESLLSQFT AWKHRQRQVG REDELMIKVS VEAGYSDQG REQVSRVFVG EVAIVDIISP PPDIGIRIQC YTRQIDRTKT IRNMPPANTT FVKFVEWGAN EMGLNFICDT S YNDQVLKN PGRSITVASA ILASIQDMYM PDVAAFVDDD ILIVKDRDKV IRPDEVTNVN SFVGIPSWSE WGVEFQCLFE PS IRVAGGV AVESLMNPSV NGNYVITALE YDLASRDRPF YIKVMGSPAA

UniProtKB: Phage protein

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Macromolecule #7: gp39 Ripcord-2

MacromoleculeName: gp39 Ripcord-2 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 21.667574 KDa
SequenceString: MNSFLKSILN TPTLTIRDDV TKLPVWKSLQ VKKVEIYSPA SVVSKPLATK DQTEAQVYTE ALDIDVKNGK IIQPVRLRIN AICPDLSTV ESIMNAFNDN TSTFAITSKS ILADKMAIMT LDVDQSPDML NAAEINMEFE QVEPPVLNEF DPAFPQDSPT Y GVQIQSLS ...String:
MNSFLKSILN TPTLTIRDDV TKLPVWKSLQ VKKVEIYSPA SVVSKPLATK DQTEAQVYTE ALDIDVKNGK IIQPVRLRIN AICPDLSTV ESIMNAFNDN TSTFAITSKS ILADKMAIMT LDVDQSPDML NAAEINMEFE QVEPPVLNEF DPAFPQDSPT Y GVQIQSLS DANLLDLGAI GDSISSAAKS LYNRVTSYF

UniProtKB: Tail fiber protein

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Macromolecule #8: gp46 Baseplate wedge 2

MacromoleculeName: gp46 Baseplate wedge 2 / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 54.629078 KDa
SequenceString: MTLPAYNSDI QQALKWLHNQ APGITGLIQR KAQWYDRFSR QFWANWERDV FHLKTANPFG LMVWCIILGT PSKGFGLYPK NSSWAFGRL RQNFIYSGTQ VPPPADASPG GNFYGGGNAE ILNLDEIRKV LQLRYVALIS NGSIAYINRM LRYIFNDDEP W DEATGLYF ...String:
MTLPAYNSDI QQALKWLHNQ APGITGLIQR KAQWYDRFSR QFWANWERDV FHLKTANPFG LMVWCIILGT PSKGFGLYPK NSSWAFGRL RQNFIYSGTQ VPPPADASPG GNFYGGGNAE ILNLDEIRKV LQLRYVALIS NGSIAYINRM LRYIFNDDEP W DEATGLYF YLMDSTGENG PVENLAIYRK DWEGMVLLSS SPRTNHVLTS TPASDADWPG VDPAASGIPV TVETASATAP DG SATVCKL TKPAGSTAYV SAPIDGPLGS GSTVTFSFFA KAGSTRFIAI QSAADFPSRA DAVFDLDSGN VISDQMLDSS VVS ARMIRL ENGWWRCVLT TKTVSSSFRA AYVAPAETNF SWIDSNSSAA IDVLIWGAQI ELGDTPTGYL ETTGAPVTMT DYVL QNAQT GTVKFTQPLP TGVEAYWTGD WKGGTAAEPA RFAVGNGTQD TFTLSDPAYI GLPTSGAFKL EYRVGPALNL SPQLI NLMN DRAVGIMPTC AGCDVKVIQE

UniProtKB: Tail fiber protein

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Macromolecule #9: gp37 Baseplate tube

MacromoleculeName: gp37 Baseplate tube / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 17.748182 KDa
SequenceString:
MINVSGFGTG IVIVSASSFP MGFSLSKFAD DESPISSKEL EPFGYEMLYD GGLFAFDKAA PLEVSVSVIA GSEDDINLRI LLNSKKGSF RFLPGIIPDM TTLVATLPDG GRTVLSNGTI IKGPAIDTIQ NTGRRKGNTY TFVFGSYLGA QTARQAISNV I QSVLEVV

UniProtKB: Phage protein

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Macromolecule #10: gp35 Sheath initiator

MacromoleculeName: gp35 Sheath initiator / type: protein_or_peptide / ID: 10 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 12.511949 KDa
SequenceString:
MSTSTIRTGT NNDILLDDNG NMVILRDVEA CAQDVRAAML MRTGENIFDV NSGVGYFEYI FSPQKSYDDA RKSIADAILS SPDVTGIEQ LDIDITGEVF GVDAKVITIH GPVTTGV

UniProtKB: Phage protein

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Macromolecule #11: gp44 Tail tip

MacromoleculeName: gp44 Tail tip / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa193
Molecular weightTheoretical: 24.201186 KDa
SequenceString: MSNISLTSAK APDRTRLIAA LDARSRRDAL DFEVMIPAQV VQYDRAENIA TIQPLITWVD TEHNAVQRHQ LVDIPVISMG AGGFHISFP IQQGDIGWIY AADRDTSQFL ESLSMSKPNT GRIHKFEHGL FIPDVFRRYT INSEDSAAMV IQSTSGATRI S IRGDNIKI ...String:
MSNISLTSAK APDRTRLIAA LDARSRRDAL DFEVMIPAQV VQYDRAENIA TIQPLITWVD TEHNAVQRHQ LVDIPVISMG AGGFHISFP IQQGDIGWIY AADRDTSQFL ESLSMSKPNT GRIHKFEHGL FIPDVFRRYT INSEDSAAMV IQSTSGATRI S IRGDNIKI TAPSNVTVDT PQANFTGNVT IANTLVVNGI NVNNHGHLEN NPPDARTKGG MIA

UniProtKB: Baseplate protein

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 12520 / Average electron dose: 34.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.75 µm / Calibrated defocus min: 0.75 µm / Calibrated magnification: 64000 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 40335
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 17175
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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