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- EMDB-63389: Structure of bacteriophage T4 protal-neck protein gp20-gp13-gp14-... -

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Basic information

Entry
Database: EMDB / ID: EMD-63389
TitleStructure of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hfq assembled in vitro in C6 symmetry
Map data
Sample
  • Complex: Complex of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hfq assembled in vitro
    • Protein or peptide: Neck protein gp13
    • Protein or peptide: Portal protein
    • Protein or peptide: RNA-binding protein Hfq
    • Protein or peptide: Neck protein gp14
KeywordsStructural protein / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / regulation of translation, ncRNA-mediated / viral genome packaging / regulation of RNA stability / viral release from host cell / virion component / viral capsid / regulation of DNA-templated transcription / RNA binding / cytosol
Similarity search - Function
Portal protein Gp20 / Bacteriophage T4, Gp14, neck protein / Bacteriophage T4-like portal protein (Gp20) / Virus neck protein / RNA-binding protein Hfq / Hfq protein / : / Sm domain profile. / LSM domain superfamily
Similarity search - Domain/homology
Portal protein / RNA-binding protein Hfq / Neck protein gp13 / Neck protein gp14
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsHan L / Mao Q / Sun L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hfq assembled in vitro in C6 symmetry
Authors: Han L / Mao Q / Sun L
History
DepositionFeb 7, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63389.png

Downloads & links

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Map

FileDownload / File: emd_63389.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.72 Å		1.05 Å/pix.
x 320 pix.
= 334.72 Å		1.05 Å/pix.
x 320 pix.
= 334.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.046 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00591
Minimum - Maximum-0.025661107 - 0.054994293
Average (Standard dev.)0.000014847677 (±0.0025812935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63389_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_63389_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hf...

EntireName: Complex of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hfq assembled in vitro
Components
  • Complex: Complex of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hfq assembled in vitro
    • Protein or peptide: Neck protein gp13
    • Protein or peptide: Portal protein
    • Protein or peptide: RNA-binding protein Hfq
    • Protein or peptide: Neck protein gp14

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Supramolecule #1: Complex of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hf...

SupramoleculeName: Complex of bacteriophage T4 protal-neck protein gp20-gp13-gp14-Hfq assembled in vitro
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T4 (virus)

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Macromolecule #1: Neck protein gp13

MacromoleculeName: Neck protein gp13 / type: protein_or_peptide / ID: 1
Details: The sequence of organism Escherichia phage T4 is not available during the biocuration, replaced by P11110 temporarily.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 35.601078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGYNPQNPK ELKDVILRRL GAPIINVELT PDQIYDCIQR ALELYGEYHF DGLNKGFHVF YVGDDEERYK TGVFDLRGSN VFAVTRILR TNIGSITSMD GNATYPWFTD FLLGMAGING GMGTSCNRFY GPNAFGADLG YFTQLTSYMG MMQDMLSPIP D FWFNSANE ...String:
MSGYNPQNPK ELKDVILRRL GAPIINVELT PDQIYDCIQR ALELYGEYHF DGLNKGFHVF YVGDDEERYK TGVFDLRGSN VFAVTRILR TNIGSITSMD GNATYPWFTD FLLGMAGING GMGTSCNRFY GPNAFGADLG YFTQLTSYMG MMQDMLSPIP D FWFNSANE QLKVMGNFQK YDLIIVESWT KSYIDTNKMV GNTVGYGTVG PQDSWSLSER YNNPDHNLVG RVVGQDPNVK QG AYNNRWV KDYATALAKE LNGQILARHQ GMMLPGGVTI DGQRLIEEAR LEKEALREEL YLLDPPFGIL VGHHHHHH

UniProtKB: Neck protein gp13

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Macromolecule #2: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 62.177188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK ...String:
MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK EGIKELRRLD PRQVQYVREI ITETEAGTKI VKGYKEYFIY DTAHESYACD GRMYEAGTKI KIPKAAVVYA HS GLVDCCG KNIIGYLHRA VKPANQLKLL EDAVVIYRIT RAPDRRVWYV DTGNMPARKA AEHMQHVMNT MKNRVVYDAS TGK IKNQQH NMSMTEDYWL QRRDGKAVTE VDTLPGADNT GNMEDIRWFR QALYMALRVP LSRIPQDQQG GVMFDSGTSI TRDE LTFAK FIRELQHKFE EVFLDPLKTN LLLKGIITED EWNDEINNIK IEFHRDSYFA ELKEAEILER RINMLTMAEP FIGKY ISHR TAMKDILQMT DEEIEQEAKQ IEEESKEARF QDPDQEQEDF SSGHHHHHH

UniProtKB: Portal protein

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Macromolecule #3: RNA-binding protein Hfq

MacromoleculeName: RNA-binding protein Hfq / type: protein_or_peptide / ID: 3
Details: The sequence of organism Escherichia phage T4 is not available during the biocuration, replaced by A7ZV41 temporarily.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 12.583903 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MWSHPQFEKG SSMAKGQSLQ DPFLNALRRE RVPVSIYLVN GIKLQGQIES FDQFVILLKN TVSQMVYKHA ISTVVPSRPV SHHSNNAGG GTSSNYHHGS SAQNTSAQQD SEETE

UniProtKB: RNA-binding protein Hfq

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Macromolecule #4: Neck protein gp14

MacromoleculeName: Neck protein gp14 / type: protein_or_peptide / ID: 4
Details: The sequence of organism Escherichia phage T4 is not available during the biocuration, replaced by P11111 temporarily.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 30.657924 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSSGM ATYDKNLFAK LENRTGYSQT NETEILNPYV NFNHYKNSQI LADVLVAESI QMRGVECYYV PREYVSPDLI FGEDLKNKF TKAWKFAAYL NSFEGYEGAK SFFSNFGMQV QDEVTLSINP NLFKHQVNGK EPKEGDLIYF PMDNSLFEIN W VEPYDPFY ...String:
HHHHHHSSGM ATYDKNLFAK LENRTGYSQT NETEILNPYV NFNHYKNSQI LADVLVAESI QMRGVECYYV PREYVSPDLI FGEDLKNKF TKAWKFAAYL NSFEGYEGAK SFFSNFGMQV QDEVTLSINP NLFKHQVNGK EPKEGDLIYF PMDNSLFEIN W VEPYDPFY QLGQNAIRKI TAGKFIYSGE EINPVLQKNE GINIPEFSEL ELNAVRNLNG IHDINIDQYA EVDQINSEAK EY VEPYVVV NNRGKSFESS PFDNDFMD

UniProtKB: Neck protein gp14

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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 recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 53.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON IV (4k x 4k) / #1 - Average electron dose: 53.0 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: FEI FALCON IV (4k x 4k) / #2 - Average electron dose: 53.0 e/Å2 / #3 - Image recording ID: 4 / #3 - Film or detector model: FEI FALCON IV (4k x 4k) / #3 - Average electron dose: 53.0 e/Å2 / #4 - Image recording ID: 5 / #4 - Film or detector model: FEI FALCON IV (4k x 4k) / #4 - Average electron dose: 53.0 e/Å2 / #5 - Image recording ID: 6 / #5 - Film or detector model: FEI FALCON IV (4k x 4k) / #5 - Average electron dose: 53.0 e/Å2 / #6 - Image recording ID: 7 / #6 - Film or detector model: FEI FALCON IV (4k x 4k) / #6 - Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3ja7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 80622
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Image processing #2

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Image processing #4

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Image processing #5

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Image processing #6

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Image processing #7

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