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- EMDB-33560: CryoEM structure of Klebsiella phage Kp9 tail complex applied wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-33560
TitleCryoEM structure of Klebsiella phage Kp9 tail complex applied with C6 symmetry
Map data
Sample
  • Virus: Klebsiella phage Kp9 (virus)
    • Protein or peptide: phage connector protein
    • Protein or peptide: phage tail tubular protein A
    • Protein or peptide: phage tail tubular protein B
    • Protein or peptide: phage type I tail fiber
KeywordsComplex / Podophage / short non-contractile tail / VIRUS
Biological speciesKlebsiella phage Kp9 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsHuang L / Xiang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure and assembly of the Klebsiella pneumoniae phage tail fibers
Authors: Huang L / Xiang Y
History
DepositionJun 8, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33560.png

Downloads & links

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Map

FileDownload / File: emd_33560.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0742 Å
Density
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.031315483 - 0.06851821
Average (Standard dev.)0.000042863896 (±0.0008137702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1074.2001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33560_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33560_half_map_2.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 : Klebsiella phage Kp9

EntireName: Klebsiella phage Kp9 (virus)
Components
  • Virus: Klebsiella phage Kp9 (virus)
    • Protein or peptide: phage connector protein
    • Protein or peptide: phage tail tubular protein A
    • Protein or peptide: phage tail tubular protein B
    • Protein or peptide: phage type I tail fiber

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Supramolecule #1: Klebsiella phage Kp9

SupramoleculeName: Klebsiella phage Kp9 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2936516 / Sci species name: Klebsiella phage Kp9 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Klebsiella pneumoniae ATCC 43816 (bacteria)
Virus shellShell ID: 1 / Diameter: 600.0 Å / T number (triangulation number): 7

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Macromolecule #1: phage connector protein

MacromoleculeName: phage connector protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage Kp9 (virus)
Molecular weightTheoretical: 58.661219 KDa
SequenceString: MAEVKLEGFA EEGAKAVYDR LKNDRQPYET RAESCAQYTI PSLFPKDSDN ASTDYTTPWQ SVGARGLNNL ASKLMLALFP MQSWMKLTI SEYEAKNLLG DAEGLAKVDE GLSMVERIIM NYIESNSYRV TLFECLKQLC VAGNALLYLP EPEGYTPMKL Y RLNSYVVQ ...String:
MAEVKLEGFA EEGAKAVYDR LKNDRQPYET RAESCAQYTI PSLFPKDSDN ASTDYTTPWQ SVGARGLNNL ASKLMLALFP MQSWMKLTI SEYEAKNLLG DAEGLAKVDE GLSMVERIIM NYIESNSYRV TLFECLKQLC VAGNALLYLP EPEGYTPMKL Y RLNSYVVQ RDAFGNVLQI VTLDKIAFNA LPEDVRSQVE AAQGEQKEDA EIDVYTHVYL NEAGDGYSKY EEVAEEVVPG SE AEYPLEE CPYIPVRMVR IDGESYGRSY VEEYLGDLKS LENLQESIVK MAMITAKVIG LVDPAGITQV RRLTAAQSGA FVP GRKQDI EFLQLEKSGD FTVAKNVSDT IEARLSYAFM LNSAVQRTGE RVTAEEIRYV ASELEDTLGG VYSILSQELQ LPLV RVLLK QLQATQQIPE LPKEAVEPTI STGLEAIGRG QDLDKLERCI AAWSALKALE GDDDLNLANL KLRIANAIGL DTAGM LLTQ EQKNALMAQQ GAQIATQQGA AALGQGMAAQ ATASPEAMAA AADSVGMQPG M

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Macromolecule #2: phage tail tubular protein A

MacromoleculeName: phage tail tubular protein A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage Kp9 (virus)
Molecular weightTheoretical: 21.374646 KDa
SequenceString: MNMQDAYFGS AAELDAVNEM LAAIGESPVT TLDEDGSADV ANARRILNRI NRQIQSKGWA FNINESATLT PDASTGLIPF RPAYLSILG GQYINRGGWV YDKSTGTDTF SGPITVTLIT LQDYDEMPEC FRQWIVTKAS RQFNSRFFGA EDVENSLAQE E MEARMACN ...String:
MNMQDAYFGS AAELDAVNEM LAAIGESPVT TLDEDGSADV ANARRILNRI NRQIQSKGWA FNINESATLT PDASTGLIPF RPAYLSILG GQYINRGGWV YDKSTGTDTF SGPITVTLIT LQDYDEMPEC FRQWIVTKAS RQFNSRFFGA EDVENSLAQE E MEARMACN EYEMDFGQYN MLDGDAYVQG LIGR

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Macromolecule #3: phage tail tubular protein B

MacromoleculeName: phage tail tubular protein B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage Kp9 (virus)
Molecular weightTheoretical: 89.081969 KDa
SequenceString: MALVSQSIKN LKGGISQQPE ILRYPEQGTL QVNGWSSETE GLQKRPPMVF IKSLGPRGYL GEDPYIHLIN RDEYEQYYAV FTGNDVRVF DLSGYEYQVR GDRSYVTVNN PKDNLRMVTV ADYTFIVNRT RQVRENQNRT NGGTFRDNVD AIINVRGGQY G RKLEVNIN ...String:
MALVSQSIKN LKGGISQQPE ILRYPEQGTL QVNGWSSETE GLQKRPPMVF IKSLGPRGYL GEDPYIHLIN RDEYEQYYAV FTGNDVRVF DLSGYEYQVR GDRSYVTVNN PKDNLRMVTV ADYTFIVNRT RQVRENQNRT NGGTFRDNVD AIINVRGGQY G RKLEVNIN GVWVSHQLPP GDNAKEDPPK VDAQAIAEAI ATLLRTAHPT WTFNVGTGFI HCIAPADTTI DILETKDGYA DQ LINPVTH YVQSFSKLPL NAPDGYMVKI VGDTSKTADQ YYVKYDKSQK VWKETVGWNI SVGLEYHTMP WTLVRAADGN FDL GYHEWK DRRAGDDDTN PQPSFVNSTI TDVFFFRNRL GFISGENIVM SRTSKYFEFY PPSVANYTDD DPLDVAVSHN RVSV LKYAV SFAEELLLWS DEAQFVLSAN GVLSAKTAQL DLTTQFDVSD RARPYGIGRN IYYASPRSSF TSIMRYYAVQ DVSSV KNAE DMTAHVPNYI PNGVYSINGS GTENFACVLT KGAPSKVFIY KFLYMDENIR QQSWSHWDFG DGVEVMAANC INSTMY MLM RNGYNVWIAA VDFKKESTDF PFEPYRFHVD AKRSYHISET AYDIETNQTV VNVKDIYGAS FAKGTVAICE SDGKITE YE PTGNSWDSTP DIRISGDVSG KNIVIGFLYD FQYVFSRFLI KQEQNDGTTS TEDSGRLQLR RAWVNYQNTG AFTVSVDN G SREFNYLVNA RVGSTGLRLG QKATTTGQYR FPVTGNALYQ KVSLSSFNAS PVSIIGCGWE GNYSRRANGI

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Macromolecule #4: phage type I tail fiber

MacromoleculeName: phage type I tail fiber / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage Kp9 (virus)
Molecular weightTheoretical: 84.120445 KDa
SequenceString: MDQDIKTVIQ YPVGTTEFDI PFDYLSRKFV RVSLVSDDNR RLLSNITEYR YVSKTRVKLL VATTGFDRVE IRRFTSASER IVDFSDGSV LRANDLNVSQ LQSAHIAEEA RDAALLAMPE DDAGNLDARN RKIVRLAPGE AGTDAINKNQ LDTTLGEAGG I LSEVKDLQ ...String:
MDQDIKTVIQ YPVGTTEFDI PFDYLSRKFV RVSLVSDDNR RLLSNITEYR YVSKTRVKLL VATTGFDRVE IRRFTSASER IVDFSDGSV LRANDLNVSQ LQSAHIAEEA RDAALLAMPE DDAGNLDARN RKIVRLAPGE AGTDAINKNQ LDTTLGEAGG I LSEVKDLQ KDMEDYLQNW GDDTTAIRGV LWVYNQGSAV GGETSFVITK EGPVLAVPYI EINGSRQYRG WHYEYDLGSK TI TLAKPLS AGDLVVCTTA ETTLPLADSL AGPTGASQIG TANGLNVQIA LDNLRSGVNV LDFMTFAERA AVLNYTGTND NSE AFRKAF ATGSRQIIVP PGRYHVKDVE IPSKVKLFGT YSYKPYNVTS DASFGTDGTI IRKVAGADNM FLWNTACAAE GVMF DGRDR TSPAIQSKSG GKISVGFFKC GFYRFDRVGN RRGAYIGCSF QFCNFNQNNI GIYNTVDGNH IGCTINANKS HGVML ETGA NSNTFTNCRN EWNEGDNWNF YGATSIQVIN ELCDRAFGYG FRISNSSVTL INVNIRRSAR TAASGAASAQ IYFESS TLK MIGVNSSVGG DDTGGSITEP SPDYFFRMAG TSEGRLEISD SRLTGYTVGL ISGTARPSVI RVINSPGWED TINEGVA RI SGGRPYIGTM PTATGPANVS PAVLGLSCGG VNTYDNDMFD IHLTIRNTNN GGHNGAILTV LLYREGGAAR ATIVRVDS R SNAVGEGDVN STSADPQQVY QVSVEVTSND ASTFNLLVST KSDNSASYRF RAKVKP

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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 / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 41926
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 63
Output model

PDB-7y1c:
CryoEM structure of Klebsiella phage Kp9 tail complex applied with C6 symmetry

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