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- EMDB-62959: unique-vertex of mature phage N4 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62959
Titleunique-vertex of mature phage N4
Map dataconf A of mature N4
Sample
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: Probable portal protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: 32 kDa protein
KeywordsComplex / VIRAL PROTEIN
Function / homologyPhage SU10 portal protein / symbiont genome ejection through host cell envelope, short tail mechanism / virion component / viral capsid / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 32 kDa protein / Probable portal protein / Major capsid protein
Function and homology information
Biological speciesEscherichia phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsLiu H / Chen W
Funding support China, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
National Natural Science Foundation of China (NSFC)32271329 China
National Natural Science Foundation of China (NSFC)32071262 China
CitationJournal: To Be Published
Title: unique-vertex of mature phage N4
Authors: Liu H / Chen W
History
DepositionJan 3, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62959.png

Downloads & links

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Map

FileDownload / File: emd_62959.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconf A of mature N4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 480 pix.
= 508.8 Å		1.06 Å/pix.
x 480 pix.
= 508.8 Å		1.06 Å/pix.
x 480 pix.
= 508.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-32.985076999999997 - 49.121574000000003
Average (Standard dev.)-0.0010446425 (±2.4641316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 508.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map2

Fileemd_62959_half_map_1.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1

Fileemd_62959_half_map_2.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage N4

EntireName: Escherichia phage N4 (virus)
Components
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: Probable portal protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: 32 kDa protein

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Supramolecule #1: Escherichia phage N4

SupramoleculeName: Escherichia phage N4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2886925 / Sci species name: Escherichia phage N4 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Probable portal protein

MacromoleculeName: Probable portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 85.642523 KDa
SequenceString: MEQNTDSMVP LPDPSQATKL TSWKNELSLQ ALKADLDAAK PSHTAMMIKV KEWNDLMRIE GKAKPPKVKG RSQVQPKLVR RQAEWRYSA LTEPFLGSNK LFKVTPVTWE DVQGARQNEL VLNYQFRTKL NRVSFIDNYV RSVVDDGTGI VRVGWNREIR K EKQEVPVF ...String:
MEQNTDSMVP LPDPSQATKL TSWKNELSLQ ALKADLDAAK PSHTAMMIKV KEWNDLMRIE GKAKPPKVKG RSQVQPKLVR RQAEWRYSA LTEPFLGSNK LFKVTPVTWE DVQGARQNEL VLNYQFRTKL NRVSFIDNYV RSVVDDGTGI VRVGWNREIR K EKQEVPVF SLFPIQTQEQ ADALQQALQL RTDNPRGYEE NVDEAIKESV RFFDETGQAT YAVQTGTTTT EVEVPLANHP TV EMLNPEN IIIDPSCQGD INKAMFAIVS FETCKADLLK EKDRYHNLNK IDWQSSAPVN EPDHATTTPQ EFQISDPMRK RVV AYEYWG FWDIEGNGVL EPIVATWIGS TLIRLEKNPY PDGKLPFVLI PYMPVKRDMY GEPDAELLGD NQAVLGAVMR GMID LLGRS ANGQRGMPKG MLDALNSRRY REGEDYEYNP TQNPAQMIIE HKFPELPQSA LTMATLQNQE AESLTGVKAF AGGVT GESY GDVAAGIRGV LDAASKREMA ILRRLAKGMS EIGNKIIAMN AVFLAEHEVV RITNEEFVTI KREDLKGNFD LEVDIS TAE VDNQKSQDLG FMLQTIGPNV DQQITLNILA EIADLKRMPK LAHDLRTWQP QPDPVQEQLK QLAVEKAQLE NEELRSK IR LNDAQAQKAM AERDNKNLDY LEQESGTKHA RDLEKMKAQS QGNQQLEITK ALTKPRKEGE LPPNLSAAIG YNALTNGE D TGIQSVSERD IAAEANPAYS LGSSQFDPTR DPALNPGIRL GN

UniProtKB: Probable portal protein

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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 44.074816 KDa
SequenceString: MLNYNAPTDG QKSSIDGANS DQMQTFFWLK KAIITARKEQ YFMPLASVTN MPKHYGKTIK VYEYVPLLDD RNINDQGIDA SGATIVNGN LYGSSKDIGN ITSKLPLLTE NGGRVNRVGF TRIAREGSIH KFGFFYEFTQ ESIDFDSDDG LMEHLSRELM N GATQITEA ...String:
MLNYNAPTDG QKSSIDGANS DQMQTFFWLK KAIITARKEQ YFMPLASVTN MPKHYGKTIK VYEYVPLLDD RNINDQGIDA SGATIVNGN LYGSSKDIGN ITSKLPLLTE NGGRVNRVGF TRIAREGSIH KFGFFYEFTQ ESIDFDSDDG LMEHLSRELM N GATQITEA VLQKDLLAAA GTVLYAGAAT SDATITGEGS TPSVVSYKNL MRLDQILTEN RTPTQTTIIT GSRMIDTKVI GA TRVMYVG SELVPELKAM KDLFGNKAFI ETQHYADAGT IMNGEVGSID KFRIIQVPEM LHWAGAGAQA TGANPGYRTS MVS GQEHYD VYPMLVVGDD SFTSIGFQTD GKSLKFTVMT KMPGKETADR NDPYGETGFS SIKWYYGILV KRPERLALIK TVAP L

UniProtKB: Major capsid protein

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Macromolecule #3: 32 kDa protein

MacromoleculeName: 32 kDa protein / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 29.2059 KDa
SequenceString: MPVLKVMFHK DTNVATVLDA SGSLSDGSVE VGTFHHPDET YPDSVTIYHG VRDLLYKRSA KDPSQTASYP NNIINMQVIS IDMKATPRL ILGTALPRVI STIEGKDVTW HVDVAGGKAP LTYKWQFKAN TVGAAFADID SGENPTAKTA TLINHAVTAE S AGTYKVIV ...String:
MPVLKVMFHK DTNVATVLDA SGSLSDGSVE VGTFHHPDET YPDSVTIYHG VRDLLYKRSA KDPSQTASYP NNIINMQVIS IDMKATPRL ILGTALPRVI STIEGKDVTW HVDVAGGKAP LTYKWQFKAN TVGAAFADID SGENPTAKTA TLINHAVTAE S AGTYKVIV TDANGTTIES SSLLVVGVQE PPEVASIVAY PSPLALSVAD DITDGKTVKF SSLPAGSLIG TLSIKTQPDS GK ATAEISG NVLTVKPVAA GDTTVVVTNG TKEVTVTVNV TE

UniProtKB: 32 kDa protein

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15466
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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