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- EMDB-38244: Open state of central tail fiber of bacteriophage lambda upon bin... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38244
TitleOpen state of central tail fiber of bacteriophage lambda upon binding to LamB
Map data
Sample
  • Complex: Bacteriophage lambda tail with LamB
    • Protein or peptide: Tip attachment protein J
KeywordsBacteriophage / caudovirales / siphoviridae / phage lambda / host recognition / LamB / cryo-EM / VIRUS
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / virion attachment to host cell
Similarity search - Function
Domain of unknown function DUF1983 / Domain of unknown function DUF3672 / Domain of unknown function (DUF1983) / Fibronectin type III protein / Tip attachment protein J / Putative phage tail protein / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tip attachment protein J
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsGe XF / Wang JW
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: To Be Published
Title: Cryo-EM structure of lambda tail with LamB
Authors: Ge XF / Wang JW
History
DepositionDec 9, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38244.png

Downloads & links

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Map

FileDownload / File: emd_38244.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0742 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1144422 - 1.8391743
Average (Standard dev.)0.0042298646 (±0.047175243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 343.74402 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38244_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_38244_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 : Bacteriophage lambda tail with LamB

EntireName: Bacteriophage lambda tail with LamB
Components
  • Complex: Bacteriophage lambda tail with LamB
    • Protein or peptide: Tip attachment protein J

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Supramolecule #1: Bacteriophage lambda tail with LamB

SupramoleculeName: Bacteriophage lambda tail with LamB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage Lambda (virus)

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Macromolecule #1: Tip attachment protein J

MacromoleculeName: Tip attachment protein J / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 124.550625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETV LGTEVKYDTP ITRTITSANI DRLRFTFGVQ ALVETTSKGD RNPSEVRLLV QIQRNGGWVT EKDITIKGKT T SQYLASVV ...String:
MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETV LGTEVKYDTP ITRTITSANI DRLRFTFGVQ ALVETTSKGD RNPSEVRLLV QIQRNGGWVT EKDITIKGKT T SQYLASVV MGNLPPRPFN IRMRRMTPDS TTDQLQNKTL WSSYTEIIDV KQCYPNTALV GVQVDSEQFG SQQVSRNYHL RG RILQVPS NYNPQTRQYS GIWDGTFKPA YSNNMAWCLW DMLTHPRYGM GKRLGAADVD KWALYVIGQY CDQSVPDGFG GTE PRITCN AYLTTQRKAW DVLSDFCSAM RCMPVWNGQT LTFVQDRPSD KTWTYNRSNV VMPDDGAPFR YSFSALKDRH NAVE VNWID PNNGWETATE LVEDTQAIAR YGRNVTKMDA FGCTSRGQAH RAGLWLIKTE LLETQTVDFS VGAEGLRHVP GDVIE ICDD DYAGISTGGR VLAVNSQTRT LTLDREITLP SSGTALISLV DGSGNPVSVE VQSVTDGVKV KVSRVPDGVA EYSVWE LKL PTLRQRLFRC VSIRENDDGT YAITAVQHVP EKEAIVDNGA HFDGEQSGTV NGVTPPAVQH LTAEVTADSG EYQVLAR WD TPKVVKGVSF LLRLTVTADD GSERLVSTAR TTETTYRFTQ LALGNYRLTV RAVNAWGQQG DPASVSFRIA APAAPSRI E LTPGYFQITA TPHLAVYDPT VQFEFWFSEK QIADIRQVET STRYLGTALY WIAASINIKP GHDYYFYIRS VNTVGKSAF VEAVGRASDD AEGYLDFFKG KITESHLGKE LLEKVELTED NASRLEEFSK EWKDASDKWN AMWAVKIEQT KDGKHYVAGI GLSMEDTEE GKLSQFLVAA NRIAFIDPAN GNETPMFVAQ GNQIFMNDVF LKRLTAPTIT SGGNPPAFSL TPDGKLTAKN A DISGSVNA NSGTLSNVTI AENCTINGTL RAEKIVGDIV KAASAAFPRQ RESSVDWPSG TRTVTVTDDH PFDRQIVVLP LT FRGSKRT VSGRTTYSMC YLKVLMNGAV IYDGAANEAV QVFSRIVDMP AGRGNVILTF TLTSTRHSAD IPPYTFASDV QVM VIKKQA LGISVV

UniProtKB: Tip attachment protein J

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 358235
FSC plot (resolution estimation)

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