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- EMDB-50186: Interface between baseplate cup and extended tail tube/sheath of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50186
TitleInterface between baseplate cup and extended tail tube/sheath of Klebsiella phage KP1 variant vB_Kpn_Lilla1
Map data
Sample
  • Virus: vB_Kpn_Lilla1 (virus)
    • Protein or peptide: x 11 types
  • Protein or peptide: x 3 types
  • Ligand: x 1 types
KeywordsBaseplate cup / baseplate wedge / fibers / VIRUS
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme ...virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / structural molecule activity / membrane
Similarity search - Function
Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / : / Long-tail fiber proximal subunit, C-terminal, second / Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 ...Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / : / Long-tail fiber proximal subunit, C-terminal, second / Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / : / Tail sheath protein Gp18-like domain I / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / : / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III / Baseplate wedge protein gp10 domain 3 / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Bacteriophage T4 gp5 C-terminal trimerisation domain / : / Tail sheath protein Gp18 domain III N-terminal region / IraD/Gp25-like / Baseplate wedge protein gp25 / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Lysozyme-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold
Similarity search - Domain/homology
IraD/Gp25-like domain-containing protein / Baseplate wedge protein gp6 / Baseplate wedge subunit / Baseplate wedge tail fiber connector / Tail sheath protein / Baseplate wedge protein gp10 / Tail tube protein / Baseplate wedge protein gp7 / Baseplate tail tube cap / Baseplate wedge subunit ...IraD/Gp25-like domain-containing protein / Baseplate wedge protein gp6 / Baseplate wedge subunit / Baseplate wedge tail fiber connector / Tail sheath protein / Baseplate wedge protein gp10 / Tail tube protein / Baseplate wedge protein gp7 / Baseplate tail tube cap / Baseplate wedge subunit / Long tail fiber proximal subunit / Baseplate subunit / Putative baseplate hub subunit / Baseplate central spike protein
Similarity search - Component
Biological speciesKlebsiella phage KP1 (virus) / vB_Kpn_Lilla1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsOrlova EV / Isupov MN
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1
Authors: Orlova EV / Isupov MN
History
DepositionApr 26, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50186.png

Downloads & links

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Map

FileDownload / File: emd_50186.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.29478946 - 0.5440083
Average (Standard dev.)0.004389434 (±0.03993818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.304 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: C3 map to 4.33 A resolution used to...

Fileemd_50186_additional_1.map
AnnotationC3 map to 4.33 A resolution used to rebuild monomers with C3 symmetry, particularly gp199.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50186_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50186_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : vB_Kpn_Lilla1

EntireName: vB_Kpn_Lilla1 (virus)
Components
  • Virus: vB_Kpn_Lilla1 (virus)
    • Protein or peptide: Baseplate subunit
    • Protein or peptide: Baseplate wedge protein gp6
    • Protein or peptide: Baseplate wedge protein gp7
    • Protein or peptide: Baseplate wedge subunit
    • Protein or peptide: Baseplate wedge tail fiber connector
    • Protein or peptide: Baseplate wedge protein gp10
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Putative baseplate hub subunit
    • Protein or peptide: Baseplate tail tube cap
    • Protein or peptide: Long tail fiber proximal subunit
  • Protein or peptide: IraD/Gp25-like domain-containing protein
  • Protein or peptide: Baseplate wedge subunit
  • Protein or peptide: Baseplate central spike protein
  • Ligand: CHLORIDE ION

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Supramolecule #1: vB_Kpn_Lilla1

SupramoleculeName: vB_Kpn_Lilla1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #3-#10, #12, #2, #1 / NCBI-ID: 2070202 / Sci species name: vB_Kpn_Lilla1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Klebsiella (bacteria)

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Macromolecule #1: Long tail fiber proximal subunit

MacromoleculeName: Long tail fiber proximal subunit / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 138.688438 KDa
SequenceString: MSDLLKQHFR ATNGLDAGGN KVINVALADR NVKTDGVSVE YVIQENTIQK YDPTRGYLTD FAVTYGRRIW IANKDIPKPA GDFNQANWT SLRVDPNWIY TVRKGEFEIQ SGQFINVDSN AAGNATLLLP LAPDEGDTIV VRDIGGRPGY NGILIKAQDT G ASIVFGES ...String:
MSDLLKQHFR ATNGLDAGGN KVINVALADR NVKTDGVSVE YVIQENTIQK YDPTRGYLTD FAVTYGRRIW IANKDIPKPA GDFNQANWT SLRVDPNWIY TVRKGEFEIQ SGQFINVDSN AAGNATLLLP LAPDEGDTIV VRDIGGRPGY NGILIKAQDT G ASIVFGES RLREVRLTRP YSQIMLTFSN GAWRASLTDF GDTAKMVVPN GIVPTQVQSG DNVVRRYTSN SEIFITLPLF AN SNDIINF TDLDGTSPIN HMTVRTFDPT ISIGTPGQTE IQVRTSGNGF LVYDSIDKIW RIFENDLRTR VRIITSDVTL MPN EHISVF GTDNNTVKTI NVTLPTDVAV GDTVTIAMNY MRKGQTVVIK ASGGDTIASN LNLLQFPKRS EYPPDAAWVQ SSSI TFNGT TSYVPVLELA YIEEKATGKS YWIITESDPT VERVDAKDNT TRARLGVIAL ATQAQANAES NAEKELAITP ETLNG RRST ETQTGIARIA TSSEVNQSTT ASYLDNVIVT PKKLNERAAT ETRRGLAEIA SNAKMDAGTD DFTIVTPKKL LYRTTS DSR LGVVQLVKTG GAPNTTNDRS SAGTGIFDHS DYKNAVTPKT LREYKATVNQ SGIVWLATDS EVRNGTPASS NIPTVVT PE ALHKKVATDG AIGLIQIATQ TEVNAGGVTN KAVTPKTLND RTATNDRTGI ARFATPGAQG EFEAGTSSTV MVNPKLLF D KFANTGRIQV NTSSGLTITG NLWDHYTINI QEASTSQRGT TTLATAAEVR TGTDAKKIVT AATLHAKTAT EGAIGLAQY ATQAQVDAGT LSDRIVPPAY LKQTIQVTES WQATDSVRGT VRLSTGDGTW KGNDTNGSTL PDNGYASKGV AVSPYELNLT LKHYLPRLG KAYDTGMLGG QTPDKYARRD IAQTISGAWS FSQDTSFSNN ISVQNIIYAN GGEVKISPTA DTGNVHVRFQ N RDGSERGI IYAEPQTASA GTLKIRVKNG TGTTAASQTY TFGGNGTLEV PNEVSTKTLR SSGNAIVGGT VMVKDVQMLA VE GLNSIFG AQSQSAFIRS RDADTQIFAQ DSTGSYPILT TKNYARLADG RYVKKAGDTM TGNLNINSSA IVITGSESWY VPT NETVIR QGSWTAEIKD ATKLKGLRGY MVPIRTPIDP ANPSTLVVTG YEEKTAAGGV LTQIGVTTNN TYQLWTPYPP TTET ADKRF AHTVWMRIYN PNLNKFDDWM RVFTSATPPT AADIGAPSSV STQVKTLEVL EWIKLGPVKI WPDRPNQTLK FEWVG D

UniProtKB: Long tail fiber proximal subunit

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Macromolecule #2: Baseplate tail tube cap

MacromoleculeName: Baseplate tail tube cap / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 38.263664 KDa
SequenceString: MIFEELADGL ENIKKSGTRI SQGKSKLTNA PTTKVAQFPA ERSAGNDSAQ DMRVHDLYRN GLLFTAYDFK GRTTPDLRSF RRDVMLSSV FDSPMSALAN SSSSTTSTAP VANILLPRSK SDVDSVSHKF NDVGDSLVTR GGGTATGVLS NVASTAVFGS I ESLTQGLM ...String:
MIFEELADGL ENIKKSGTRI SQGKSKLTNA PTTKVAQFPA ERSAGNDSAQ DMRVHDLYRN GLLFTAYDFK GRTTPDLRSF RRDVMLSSV FDSPMSALAN SSSSTTSTAP VANILLPRSK SDVDSVSHKF NDVGDSLVTR GGGTATGVLS NVASTAVFGS I ESLTQGLM ADNGEQIYNT ARSMYAGPDN RTKVFTWDLT PRSADDLIQI IRIYEIFNYY SYGVTGNSSY AKEVKAAIDE WY KGTLKSA APDGAKVENT VFEQITSFLS NVIVVSNPTI WTVRNFGYST SMDGREDIFG PCQIQSIRFD KTPNGHFNGL AIA PNLPST FTLEITMREI LTLNRGNVYI GGIE

UniProtKB: Baseplate tail tube cap

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Macromolecule #3: Baseplate subunit

MacromoleculeName: Baseplate subunit / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 33.716129 KDa
SequenceString: MFTLEEFKSQ AADIDFQRTN MFSVVFATVP SSKTQALLND FGGELYNNMG LDGNWLGLTP GEFNQGITTI VTQGTRQVVR KSGVNTFMI GAMTQRVVQS LLGEFTVGTY LLDFFNMAFP TAGLMVYSAK IPENRLSYEM DKFHNAPNIK ITGRDMEPLV L SFRMDPEA ...String:
MFTLEEFKSQ AADIDFQRTN MFSVVFATVP SSKTQALLND FGGELYNNMG LDGNWLGLTP GEFNQGITTI VTQGTRQVVR KSGVNTFMI GAMTQRVVQS LLGEFTVGTY LLDFFNMAFP TAGLMVYSAK IPENRLSYEM DKFHNAPNIK ITGRDMEPLV L SFRMDPEA SNYRAMQDWV NAVEDPVTGL RGLPQDVECD IQVNLHARNG LPHTVCLFSG AMPVACGAPE FTYDGENTIA VF DVTFAYR SMQTGSVGKQ AAMDWLEDKA IQKIETINPN QGLSASASRL SRLGGAGGGI SNITTTTSRI I

UniProtKB: Baseplate subunit

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Macromolecule #4: Baseplate wedge protein gp6

MacromoleculeName: Baseplate wedge protein gp6 / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 73.689242 KDa
SequenceString: MAIKEPLNYQ LTRTANAIPD AFTGATFDEI KNQLINWLSG QKEFQDFDFA GSRLNVLLDL LAYNTLYIQQ FGNTALYESF IGTANLRSS VVQAAQQNGY LPSSKSAATA SIMLEVTHPN PEPAIKIPRG TKFLAYARDS SVDPYNFVVT ENVIALRDTS A PEGVNRYL ...String:
MAIKEPLNYQ LTRTANAIPD AFTGATFDEI KNQLINWLSG QKEFQDFDFA GSRLNVLLDL LAYNTLYIQQ FGNTALYESF IGTANLRSS VVQAAQQNGY LPSSKSAATA SIMLEVTHPN PEPAIKIPRG TKFLAYARDS SVDPYNFVVT ENVIALRDTS A PEGVNRYL PIVNLAQGRI IRTQLSYDPK KPIVIRDQSI DRKQVKLWVD GAEWTNWTDR SMVHASSIST IYYMRETVDG NT EFFFGEG VAEASVAGGV LESNFIGGLK PTKGAQVVIE YIRTDGESAN GATDFSYADT LQYIVVNKII ENWSDSPDYV GAD GGGEPE DIERIRELAQ IKRESQMRCV SKTDYESFVS SRFGSIVQAV QCFTDQDKPG YAFIAIKPKS GLQLTAVQRE DIQD YLRPF CLAPITPSVM SPDYLFIRHN IKASYALNKL QESEQWLQSK IIDSINRYYV DEVEMFNKNF SKSKLLTYID DTDHS IIGS SVDIQMVREI VNYFTLPSAG IKYYNTITPR TLRSGDLVFT VTPTADSYPV NIVGTDPDKN GKGNMVIGPF KPGDIK ENT HIQPYTEDDF DRTTNGERTR WYKIGEVDYY GDNIYWSLGA IGADPLQFED QSIELYSTPT QDIVFARDGT LIVFEND LR PQYTTIKLEP ITQ

UniProtKB: Baseplate wedge protein gp6

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Macromolecule #5: Baseplate wedge protein gp7

MacromoleculeName: Baseplate wedge protein gp7 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 119.645719 KDa
SequenceString: MTIAPFVTSL RIHKLSANQV NIRWDDVGAN FYYFVELAET RNRAGEVIPA DNLSWSSLGY TADNDWFEQN RIEPLTYYKM RVQTTSAGF EPSEWVETEE FQTFEENAYT FEHMQEFSLV KEFIKQKFSL NNMSYVNFNT SAMMASLMTE SFQFSPEYSH L SAIENFVV ...String:
MTIAPFVTSL RIHKLSANQV NIRWDDVGAN FYYFVELAET RNRAGEVIPA DNLSWSSLGY TADNDWFEQN RIEPLTYYKM RVQTTSAGF EPSEWVETEE FQTFEENAYT FEHMQEFSLV KEFIKQKFSL NNMSYVNFNT SAMMASLMTE SFQFSPEYSH L SAIENFVV GESGYHEIQG PIEAVCVDKN RTMLGEIDGI LYLFERFQHM VKVSNDKGQN WQYVQLFNDR VGNPVSRVVI YQ SKTTSYV LGYDKIFYGR KSSDVRWSSN EVKFSDNEVT FAKLGDQLKL GFEVELFGTY ASLPADVTKY AEAFTCNDDY LYV VAKDTV RKVKLKDAPI DTDPLSPTFG EKVFEKEVSH ITGNPKSVCF KMDSVGGKIF ALITGEVKTL GLDPTDPRNV VDSA TKGVY VYQEGTNTWK RVFGNTDEEK RRIEHLWTSM STDGKEIFFS SANFKTTEYA QDIELETKYP ELISTAVKNV NPIQY HSDK HYHMMSFRAD EFSRWETFVP GPMRFYAEPW FVWMAREGNR CWISTADHAV VIYNDILYQK RVDAAAQGTT ERILSE VWD KGDATFYCPP VSFNGFLQYA SGIMFHEPDG KLIGYYAFDY RVRDQVTLNW KPTDVMFKAF LQNQTREEDW TPEHTPG LR DPDLRPYLTK MMPDSYLLQD SNFEHFCKYY LQFLSDGNGT HYNSLVNLVK NKYPREENAW EYLWSEVYKR NIYLSKDA R DAVVRFFEAR KNDFYATKGI EDSYKFLFKL LYNEDVEIDI ESKNTTEYDI IVESTNISDD LVGRTIYTAS GRSNVTYIE REYRDGRLLW RITIHNLSGR FIEGQEIKSE RTDFEGIIVQ GVRGKDMLSN NIDYINRSRS YYVMKIKSQL PTSRFRDDVL RFVHPVGFG FIGITLLTMF INSGLNMKHV ETIINKLKNY KWDAGLPSVY PDRVAIIASD DTIERDPITN EPRYSSRAQA G EPFPLPAN YNQENNNSVI AGQNPGQRRK PLSPTFDQSA VTFANYRDLV NQRLKDDAGN PRDPENPTQV KIDE

UniProtKB: Baseplate wedge protein gp7

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Macromolecule #6: Baseplate wedge subunit

MacromoleculeName: Baseplate wedge subunit / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 38.704387 KDa
SequenceString: MSNSTRASST RSTIYRAIIT SKFRTEKMYT FYKSIGPGTD QNTLYVSFGK STPWSDNESE PGFAPPYPAD NEDGVVDIWT NMMGAVKIE SSMLDCVVPR RDWGDTRYPN PRTFLIGDIV VANSAPYNRT DAGFGWMVYR CIDVPKNGMC SIGNLTSKEE C IKLGGKWT ...String:
MSNSTRASST RSTIYRAIIT SKFRTEKMYT FYKSIGPGTD QNTLYVSFGK STPWSDNESE PGFAPPYPAD NEDGVVDIWT NMMGAVKIE SSMLDCVVPR RDWGDTRYPN PRTFLIGDIV VANSAPYNRT DAGFGWMVYR CIDVPKNGMC SIGNLTSKEE C IKLGGKWT PSTISGSAPR GRGDANGTVD LGDGYLWEYL YEIPADVSIN RCTNEYIVVP WPEEIEESPA RWGFQNNLTW QQ NDFNLIY RMKCNTIRFK AYLDAVYFPE FSLPGNTGFR QLSIITNPLE VKPMPNSPNV KAEKGWYSAS GLERQSGEMI YME NRQPII RSMDQTEELN LIFEF

UniProtKB: Baseplate wedge subunit

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Macromolecule #7: Baseplate wedge tail fiber connector

MacromoleculeName: Baseplate wedge tail fiber connector / type: protein_or_peptide / ID: 7 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 32.380195 KDa
SequenceString: MYTDKGKKII DVGEIGNAST GDILYDGGVK INDNFDAIYN AFADQRLFAA GGGALNQKIH ATSYYQKIKF GDANSAGTVP MGSCIDADC SEGAVQIRLS KGKAGEAVFV VNSNGSASKA RSIKITTNGE GVADAFKDGS RELIINTPRC RIELWCVEVK A NGAAVWDY ...String:
MYTDKGKKII DVGEIGNAST GDILYDGGVK INDNFDAIYN AFADQRLFAA GGGALNQKIH ATSYYQKIKF GDANSAGTVP MGSCIDADC SEGAVQIRLS KGKAGEAVFV VNSNGSASKA RSIKITTNGE GVADAFKDGS RELIINTPRC RIELWCVEVK A NGAAVWDY SISSMFGSTY SPLEATYNLT SSPINIRLGY NDDYSTVKLL LSFSANPGGQ TIKRQSSEVM LMIDPTITSS AP NGRVFDT EYAVLRSGES SENEKMYSIS YSINAQKDLI CTASTSYGNA RLAVKVIATQ TVGVSQ

UniProtKB: Baseplate wedge tail fiber connector

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Macromolecule #8: Baseplate wedge protein gp10

MacromoleculeName: Baseplate wedge protein gp10 / type: protein_or_peptide / ID: 8 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 66.71207 KDa
SequenceString: MKQNLIVGQS VDDGSGDYLR KGGLKINNNF DDLYSELGDG SVPFAAGAWK TFKASPTGTT LNAKFGQAFA INTQAARVNV QLPKGTAND YNKVIKLRDV WSTWRLSPIT VIPAQGDTLK GSASPKIFNT NFQDLELVYC APGRWEYIEN KTVDKLTNGN L STVAKKSI ...String:
MKQNLIVGQS VDDGSGDYLR KGGLKINNNF DDLYSELGDG SVPFAAGAWK TFKASPTGTT LNAKFGQAFA INTQAARVNV QLPKGTAND YNKVIKLRDV WSTWRLSPIT VIPAQGDTLK GSASPKIFNT NFQDLELVYC APGRWEYIEN KTVDKLTNGN L STVAKKSI IATAGQTDFL NIFDGVEYNE DSLNVYRRGN ILYYGETSVM DKANADYGSP GTVAGQLVEL NGKDIRLKVP CV EGEVITF ETFLDGIGVY RSSYNKLAIQ IRDSAQTTSQ TIPGSMIVDN LATLRRITLD DMGVLPGVGV NPNSLEISLN GKE LLEAGT AGLPLFYCEG AEGGYAEDCI NNGGQWVNSN QDYRLEFDST GTNVEAIIFG EAFEDKDLLT VRWFNNNIGT TMDI DDIMA ETDQVYMNAE QLVTLKNRIE YTNYDEPNQK NMRPVADDIM IKVNNIAAFF DVIYPIGTIY ENAHNHANPA DYMGF GVWK LYSQGRVTAG WNNDSSDPYF SRNNNNLNEN GQPSLTAGGT VGDLTFTLGK EHIPELMSRD KVLISDPEHG SVVIGG CQL DPDAQGPGYS KYREDTVAVN NGVVPNDITK IQPTITVYRW IRVG

UniProtKB: Baseplate wedge protein gp10

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Macromolecule #9: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 9 / Number of copies: 42 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 71.695094 KDa
SequenceString: MPLVSPGIEL KETSVQSTVV LNATGRAAIV GKFQWGPAYQ VTQITNEVEL VDMFGGPNNQ TADYFMSAMN FLQYGNDLRT VRVVNREAA KNASPLVDNI EWEITTAGSN YEVGDKITVK YADQVVDDTG SVTEVDSDGK IKSVFIPTSK IIAYAKSINQ Y PDLGSSWT ...String:
MPLVSPGIEL KETSVQSTVV LNATGRAAIV GKFQWGPAYQ VTQITNEVEL VDMFGGPNNQ TADYFMSAMN FLQYGNDLRT VRVVNREAA KNASPLVDNI EWEITTAGSN YEVGDKITVK YADQVVDDTG SVTEVDSDGK IKSVFIPTSK IIAYAKSINQ Y PDLGSSWT TTITSQSSGV SAVITLGKII SDSTVLLTEP ETAHEEMTKT EFQTALAKYK MPGIVAAYPG ELGNQLEIEI VS KAAFDKG EQLTIYPAGG KRASTAKAVF GYGPQTDTQY AIIVRRDGAV VESAVLSTSR QDKDIYGNNI FMDDYFSKGS SRY IFATAQ GWPEGFAGVI RLGGGVSANE SVTAGDLIQG WDLFGDREAL RVNLLIAGAC AGETDEIAST VQKHVSSIAD ERQD CLALI SPPRSTIVNI PLTRAVDNLI DWRQGEGSYD SANMNINTTY AAIDGNYKYQ YDKYNDVNRW VPLAADIAGL CARTD DIAQ PWMSPAGYRR GQILNCIKLA IEPRQAHRDR MYQAGINPVT GQGTGDGFIL FGDKTATTVP TPFDRINVRR LFNMLK NNI GDSSKWQLFE LNDNFTRSSF RMETSQYLAG IKALGGVYDF RVVCDTTNNT PAVIDRNEFV ASFYIKPARS INYITLN FV ATATGADFDE LIGP

UniProtKB: Tail sheath protein

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Macromolecule #10: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 10 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 18.633738 KDa
SequenceString:
MELTDITRAF ESGDFARPNL FEVEIPYLGR NFSFKCKAAP MPAGIVEKVP VGYMNRKINV AGDRTYDDWT VTIYNDDKHE VRKAIIAWQ AQAHAQGNDI SGMTPADYKK VATVRQFSRD GKTITNEHTI TGLWPTNVGE VQMDWDSNNE VETFETTFAI D WWE

UniProtKB: Tail tube protein

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Macromolecule #11: IraD/Gp25-like domain-containing protein

MacromoleculeName: IraD/Gp25-like domain-containing protein / type: protein_or_peptide / ID: 11 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 15.38236 KDa
SequenceString:
MSNIDKLYSD LDPEMRLAWD TDVSKTVGAR SVKNSLLGII TTRKGSRPFD PEFGCDITNE LFENMTPLTG DTIKRNIVSA VRNYEPRIN RLSVDVLPLY DDNAIIVTVQ FSIVDDPDTL ERIRIQMRSN ANSSSRV

UniProtKB: IraD/Gp25-like domain-containing protein

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Macromolecule #12: Putative baseplate hub subunit

MacromoleculeName: Putative baseplate hub subunit / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 43.526016 KDa
SequenceString: MTTQRLGYPN ISIKLYSGYD AWLANRFVEL AATFITLTMR DSLRGTNEGL LQFYDSKNMH TRMNGDELVQ ISVANSNTSR TQTRIYGIK HFTVGVDDKG DSIITLQLGT LHDIMNLKFS RAFFSSAYET IKEMIGAMYV DQPLIAPPIN GINAYVPRVP W TSTLKDYL ...String:
MTTQRLGYPN ISIKLYSGYD AWLANRFVEL AATFITLTMR DSLRGTNEGL LQFYDSKNMH TRMNGDELVQ ISVANSNTSR TQTRIYGIK HFTVGVDDKG DSIITLQLGT LHDIMNLKFS RAFFSSAYET IKEMIGAMYV DQPLIAPPIN GINAYVPRVP W TSTLKDYL RYVRNVGIST DNDQFIFAWE DITGINMMDY ESMISQDPNV FMFGAPQTIG QFAAGLKYPL AWDFEWLVKS NR YNRNPMK NATFYAHSFV DKDVTRIING EGQNSVFINR SGGYSDMIFR NGYEEALRIS TMAQYDGYAQ TKCYGNFELT PGM KINFVD LKDQFRTDFY IDEVIHEISN NTSITNLYMF TNGSALEPVD LIKVKNELKR DSSY

UniProtKB: Putative baseplate hub subunit

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Macromolecule #13: Baseplate wedge subunit

MacromoleculeName: Baseplate wedge subunit / type: protein_or_peptide / ID: 13 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 24.69342 KDa
SequenceString: MLFSFFSPID YSAKTVKGAK AKAIPTADIF RNYRKYFDTV AENYLLQTYY ISGAPRPEEL AYILYGNSQL YWILLMCNNV YDPFRDWIK TQDACYQFAQ QKYADVGGDQ ILYHVDANGN RYYNLEQYPE NSGIWYDKGD FNHQYPQYTG ALAGVDIYED S IIENEKLR ...String:
MLFSFFSPID YSAKTVKGAK AKAIPTADIF RNYRKYFDTV AENYLLQTYY ISGAPRPEEL AYILYGNSQL YWILLMCNNV YDPFRDWIK TQDACYQFAQ QKYADVGGDQ ILYHVDANGN RYYNLEQYPE NSGIWYDKGD FNHQYPQYTG ALAGVDIYED S IIENEKLR QINIINPSDI EAFLSDIIRE MEKAPDSEYE SGRYKSQTTI GEVL

UniProtKB: Baseplate wedge subunit

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Macromolecule #14: Baseplate central spike protein

MacromoleculeName: Baseplate central spike protein / type: protein_or_peptide / ID: 14 / Number of copies: 3 / Enantiomer: LEVO / EC number: lysozyme
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 63.317457 KDa
SequenceString: MIEMNDSLKW FTGVVEDRQD PLKQGRVRVR VYGLHPFEKV QGAITGLPTE DLPWMSVIQP TNSAGISGVG SSITGMVEGT SVFGLWLDE FKTAGLVIGT YSAHRKTKPN YTEGFSDPTG QYPRQVGSDT NPLVQGDETG YSAIPNIIQD RNLDIGINPD D ADLSDIPE ...String:
MIEMNDSLKW FTGVVEDRQD PLKQGRVRVR VYGLHPFEKV QGAITGLPTE DLPWMSVIQP TNSAGISGVG SSITGMVEGT SVFGLWLDE FKTAGLVIGT YSAHRKTKPN YTEGFSDPTG QYPRQVGSDT NPLVQGDETG YSAIPNIIQD RNLDIGINPD D ADLSDIPE DPNPAITITD MLNRDEGLRL KVYWDTEGYP TVGIGHLIMA QKVRDMSVIN KTLSNQVGRT VTGNPGIITM DE AVALFKQ DRDKMLSDIK TNSRVGPVYA KVNKSRQMAL ENMSFQMGVG GLAKFGKMLD AMLIGDWKTA YTEARNSVWF NQT KGRASR VSMIILTGNM ESYGVPAPKP EGKNLSAAYV EPKSGGNPED PWTPEDSRIL FKEPESSYNG QYPYVHTMET ESGH IQEFD DTPGYERYRI VHPTGSYEEV APDGRRTRKT VADLYDMTQG DGNILISGDK KVNVGGNETY YNMYNRRQQI DGDNT LYVR GNETKTIEGD GTIFVKGNIK IVVEGNADIQ VNGDATTKVD GNHDVTVGGN LTWQVAGTVN WNVGGAWTET MASMSS IAQ GQYTVDGSRI DVG

UniProtKB: Baseplate central spike protein

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Macromolecule #15: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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 / Details: 100mM NaCl, 8mM MgSO4, 50mM Tris-HCl
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 92.0 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
DetailsKlebsiella phage KP1 variant vB_Kpn_Lilla1

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 78.7 K / Max: 93.6 K
DetailsAlignment procedure: EPU Autocoma and Autosrigmate Residual tilt (if alignment procedure is coma free, mrad): 68 Software used to collect images EPU 2.4, Tomo 5.13 Film/CCD/Direct electron detector model*: post GIF K3
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 4 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 83505 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
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: 34529
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2415
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 200 / Avg.num./class: 60
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9f4a:
Interface between baseplate cup and extended tail tube/sheath of Klebsiella phage KP1 variant vB_Kpn_Lilla1

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