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- EMDB-33583: CryoEM structure of Klebsiella phage Kp7 tail complex applied wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-33583
TitleCryoEM structure of Klebsiella phage Kp7 tail complex applied with C6 symmetry
Map data
Sample
  • Virus: Klebsiella phage Kp7 (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: tail adaptor protein
KeywordsComplex / Podophage / short non-contractile tail / VIRUS
Biological speciesKlebsiella phage Kp7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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 9, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33583.png

Downloads & links

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Map

FileDownload / File: emd_33583.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 1000 pix.
= 1170. Å		1.17 Å/pix.
x 1000 pix.
= 1170. Å		1.17 Å/pix.
x 1000 pix.
= 1170. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.033874143 - 0.07529607
Average (Standard dev.)0.000018101957 (±0.00073455786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1170.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33583_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_33583_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 Kp7

EntireName: Klebsiella phage Kp7 (virus)
Components
  • Virus: Klebsiella phage Kp7 (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: tail adaptor protein

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Supramolecule #1: Klebsiella phage Kp7

SupramoleculeName: Klebsiella phage Kp7 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2936515 / Sci species name: Klebsiella phage Kp7 / 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 Kp7 (virus)
Molecular weightTheoretical: 58.339309 KDa
SequenceString: MDIRGGASYS GKKSKIPELW EKLSRKRNEF LDRAKHYARL TLPYLLNEPG NNESAQNGWQ GTGAQATNHL ANKLAQVLFP AQRSFFRVD LTVKGEKALL ERGYQKTKLA TVFAKIETQA MKALDARQFR PAVVEAFKHL LVAGNCMLYK PVKSANDPAG P ISCIPMHH ...String:
MDIRGGASYS GKKSKIPELW EKLSRKRNEF LDRAKHYARL TLPYLLNEPG NNESAQNGWQ GTGAQATNHL ANKLAQVLFP AQRSFFRVD LTVKGEKALL ERGYQKTKLA TVFAKIETQA MKALDARQFR PAVVEAFKHL LVAGNCMLYK PVKSANDPAG P ISCIPMHH YAVQRDTNGQ LMDIILLQEK ALRTFEPALR AVIQAARKGK QLKDSDNVKL YTHACYEGDG FWKVQQSADD LP VGKSSRV KADKLPFMVL TWKRSYGEDW GRPLCEDYSG DLFVVQFLSE AVARGAALMA DIKYLIRPGA QTDVEHFVNS GTG EVITGV EEDIHIVQLG KYADLTPIDA VLEKYVRRIG VVFMMESLVR RDAERVTALE IQRDAMEVEQ SLGGAYSLFS VTMQ QPMAI WGLQENAGSF GSEFIDPVII TGIEALGRMA ELDKLAQFSN YMNLPTTWPE WAQDAIKPTE YMDWVRGQIS ADFPF LMSE EEAAAAAEQA QEQQADQTLN EGVAQAIPQV INQGLQEL

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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 Kp7 (virus)
Molecular weightTheoretical: 27.228775 KDa
SequenceString: MPIQSDTPSI MAESQFNSLS TKLDAVNLCM RAIGRSGVDN LTSGDLDAED ADTMIDIVSQ RLQYNDGKGW WFNREPRWSF APDSNGEVV LPNNTLQVLQ AYTLNTRKID ITIRAGRLYS TTLHSFDVSP LVGPDGFIWL DLMLMLPFEH MPLNVLQAIA Y QAAAEFIV ...String:
MPIQSDTPSI MAESQFNSLS TKLDAVNLCM RAIGRSGVDN LTSGDLDAED ADTMIDIVSQ RLQYNDGKGW WFNREPRWSF APDSNGEVV LPNNTLQVLQ AYTLNTRKID ITIRAGRLYS TTLHSFDVSP LVGPDGFIWL DLMLMLPFEH MPLNVLQAIA Y QAAAEFIV SKDADQTKLQ MHMQMAANLH TGMQVEESKQ NRLNMLVHNP TQRNFGIMAG GPNNTAGFDH SPYDRYPVRP WR W

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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 Kp7 (virus)
Molecular weightTheoretical: 87.904539 KDa
SequenceString: MEVQGSLGRQ IQGISQQPAS VRLPGQCTDA INCSMDVVEG TKSRPGTVHI ARLGDLGLIQ DNTNIHHYRR GDDVEEYWMI TNPLGIPDI FDKQGRKCTV TETEGAASYF NSNNPRVDYK FFTVGDTTFV VNRTKIVRAR ADKTPAVGGT ALVFSAYGQY G TNYQIIIN ...String:
MEVQGSLGRQ IQGISQQPAS VRLPGQCTDA INCSMDVVEG TKSRPGTVHI ARLGDLGLIQ DNTNIHHYRR GDDVEEYWMI TNPLGIPDI FDKQGRKCTV TETEGAASYF NSNNPRVDYK FFTVGDTTFV VNRTKIVRAR ADKTPAVGGT ALVFSAYGQY G TNYQIIIN GVKAAEYKTA SGGSASDVET IRTEVIAEQL YTNLLTWAGA SDYSISRMGT TIVISSLSGA SFTVDTEDGS KG KDLVAIQ YKVTSTDLLP SKAPVGYLVQ VWPTGSKPES RYWLKAEAAD GNLVTWQETL GADEVLGFDG STMPYIIERT NIV GGIAQF TIKQGYWDDR AVGDELTNPM PSFVDQSLSD IFMVQNRLCL AAGESCIMSR TSYFFQFFRQ TVLSAVDTDP IDVF ADASE VYALKHAKVL DGDTVLFSDN AQFILPGDKP LTKATALLRP TTTFEVDTNV APVVTGEAVM FATKDGAYSN IREFY TDSY SDTKKAQPVT SHVNKLIRGG IYHMASSTNF NRLFALSEDN RSRVFVYDWL WQGTDKVQSA WHKWEFYGAT IGGLYY SGE TLYLIIKRND GVFLEAMYMG DPLLSGSDQV RMDRTVTVSL TWDEATLSWK SSPLPWVPTQ VEMLEAVLTN GDPAYLG GA FLFEYDANTR ILSTKYGLGD TSQIWAAKVG QMYKVEFVPT DVIIRDSQDR VSYQDVPVIG LVHLNLDRYP DFTVEITN R KSGAVRVAKA SNRVGGARNN VVGYVKPTSG TFSFPLRALS TDVEYRIISI SPHTFQLRDI EWSGSYNPTR KRV

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Macromolecule #4: tail adaptor protein

MacromoleculeName: tail adaptor protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage Kp7 (virus)
Molecular weightTheoretical: 36.062914 KDa
SequenceString: MSYSYVERTG DGVATTFNFA FTGKGKGYLL ANQIYVERWD GASWQSATGW SLSGTNQITF LTPLANGQVI RIRRIAGKDY PFAQFEPGV MLDMASLNNT FIHLLEITQE LLDGFYPDGF YLKQDLNMGW NKIVNLMPGT DGGHAVNKTQ LDTLSSHVDD V DQKHTIWN ...String:
MSYSYVERTG DGVATTFNFA FTGKGKGYLL ANQIYVERWD GASWQSATGW SLSGTNQITF LTPLANGQVI RIRRIAGKDY PFAQFEPGV MLDMASLNNT FIHLLEITQE LLDGFYPDGF YLKQDLNMGW NKIVNLMPGT DGGHAVNKTQ LDTLSSHVDD V DQKHTIWN DRQDQQIDGL LKAFDSNISY RTAPWTYEAA GGETMVFPPF YFASALVWRD GAYQDQQAGA FEIDNNVITL AD PPLRAGE RVSVLVGSYI TPADPGSWEW IHVAANGTTT SVDLGVSVSD IDDVTLDGLS QGRSNYTLTG TVLDFGEVIP ECT VGARVQ LA

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 26075
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 47
Output model

PDB-7y22:
CryoEM structure of Klebsiella phage Kp7 tail complex applied with C6 symmetry

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