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- EMDB-33507: Cryo-EM structure of Klebsiella phage Kp9 type I tail fiber gp42 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33507
TitleCryo-EM structure of Klebsiella phage Kp9 type I tail fiber gp42 in vitro
Map data
Sample
  • Complex: Klebsiella phage Kp9 type I tail fiber protein gp42
    • Protein or peptide: Tail fiber protein
KeywordsPhage type I tail fiber / VIRAL PROTEIN
Biological speciesKlebsiella phage Kp9 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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
DepositionMay 31, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33507.png

Downloads & links

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Map

FileDownload / File: emd_33507.map.gz / Format: CCP4 / Size: 30.5 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 200 pix.
= 214.84 Å		1.07 Å/pix.
x 200 pix.
= 214.84 Å		1.07 Å/pix.
x 200 pix.
= 214.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.0728696 - 0.13056797
Average (Standard dev.)0.00031850775 (±0.0045344653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.84001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Klebsiella phage Kp9 type I tail fiber protein gp42

EntireName: Klebsiella phage Kp9 type I tail fiber protein gp42
Components
  • Complex: Klebsiella phage Kp9 type I tail fiber protein gp42
    • Protein or peptide: Tail fiber protein

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Supramolecule #1: Klebsiella phage Kp9 type I tail fiber protein gp42

SupramoleculeName: Klebsiella phage Kp9 type I tail fiber protein gp42 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Trimer of tail fiber proteins
Source (natural)Organism: Klebsiella phage Kp9 (virus)

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Macromolecule #1: Tail fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage Kp9 (virus)
Molecular weightTheoretical: 84.120445 KDa
Recombinant expressionOrganism: Escherichia (bacteria)
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 R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 74361
Initial angle assignmentType: OTHER
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: 124
Output model

PDB-7xy1:
Cryo-EM structure of Klebsiella phage Kp9 type I tail fiber gp42 in vitro

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