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- EMDB-63388: Structure of bacteriophage T4 neck protein gp13 and gp14 and Hfq ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63388
TitleStructure of bacteriophage T4 neck protein gp13 and gp14 and Hfq assembled in vitro in C6 symmetry
Map data
Sample
  • Complex: Complex of bacteriophage T4 neck protein gp13 and gp14 and Hfq assembled in vitro
    • Protein or peptide: Neck protein gp13
    • Protein or peptide: RNA-binding protein Hfq
    • Protein or peptide: Neck protein gp14
KeywordsStructural protein / VIRAL PROTEIN
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of RNA stability / virion component / regulation of DNA-templated transcription / RNA binding / cytosol
Similarity search - Function
Bacteriophage T4, Gp14, neck protein / Virus neck protein / RNA-binding protein Hfq / Hfq protein / : / Sm domain profile. / LSM domain superfamily
Similarity search - Domain/homology
RNA-binding protein Hfq / Neck protein gp13 / Neck protein gp14
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 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 neck protein gp13 and gp14 and 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_63388.png

Downloads & links

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Map

FileDownload / File: emd_63388.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.)
1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0109
Minimum - Maximum-0.0017451007 - 1.5816232
Average (Standard dev.)0.0013584832 (±0.025709195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63388_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_63388_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 : Complex of bacteriophage T4 neck protein gp13 and gp14 and Hfq as...

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

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Supramolecule #1: Complex of bacteriophage T4 neck protein gp13 and gp14 and Hfq as...

SupramoleculeName: Complex of bacteriophage T4 neck protein gp13 and gp14 and 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: RNA-binding protein Hfq

MacromoleculeName: RNA-binding protein Hfq / type: protein_or_peptide / ID: 2
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 #3: Neck protein gp14

MacromoleculeName: Neck protein gp14 / type: protein_or_peptide / ID: 3
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 recordingFilm or detector model: GATAN K3 (6k x 4k) / 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

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

1hk9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 381536
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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