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- EMDB-61909: core proteins of mature T7 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61909
Titlecore proteins of mature T7
Map datacore proteins of T7
Sample
  • Virus: Escherichia phage T7 (virus)
    • Protein or peptide: Protein 6.7
    • Protein or peptide: Internal virion protein gp14
    • Protein or peptide: Internal virion protein gp15
    • Protein or peptide: Peptidoglycan transglycosylase gp16
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / lytic transglycosylase activity / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / peptidoglycan metabolic process / symbiont entry into host / T=7 icosahedral viral capsid / virion component ...symbiont genome ejection through host cell envelope / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / lytic transglycosylase activity / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / peptidoglycan metabolic process / symbiont entry into host / T=7 icosahedral viral capsid / virion component / killing of cells of another organism / hydrolase activity / defense response to bacterium / host cell plasma membrane / membrane
Similarity search - Function
Bacteriophage T7-like, protein 6.7 / Bacteriophage T7-like, protein 6.7 / Internal virion protein Gp16 / Internal virion protein Gp14 / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Internal virion protein gp14 / Peptidoglycan transglycosylase gp16 / Protein 6.7
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiu HR / Chen WY
Funding support China, 6 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)32371263 China
National Natural Science Foundation of China (NSFC)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
CitationJournal: To Be Published
Title: core proteins of mature T7
Authors: Liu HR / Chen WY
History
DepositionOct 13, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61909.png

Downloads & links

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Map

FileDownload / File: emd_61909.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcore proteins of T7
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 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: 2.0
Minimum - Maximum-11.324947999999999 - 19.307162999999999
Average (Standard dev.)0.004073098 (±0.90823567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61909_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_61909_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 : Escherichia phage T7

EntireName: Escherichia phage T7 (virus)
Components
  • Virus: Escherichia phage T7 (virus)
    • Protein or peptide: Protein 6.7
    • Protein or peptide: Internal virion protein gp14
    • Protein or peptide: Internal virion protein gp15
    • Protein or peptide: Peptidoglycan transglycosylase gp16

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Supramolecule #1: Escherichia phage T7

SupramoleculeName: Escherichia phage T7 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10760 / Sci species name: Escherichia phage T7 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Protein 6.7

MacromoleculeName: Protein 6.7 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 9.354512 KDa
SequenceString:
MCFSPKIKTP KMDTNQIRAV EPAPLTQEVS SVEFGGSSDE TDTEGTEVSG RKGLKVERDD SVAKSKASGN GSARMKSSIR KSAFGGKK

UniProtKB: Protein 6.7

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Macromolecule #2: Internal virion protein gp14

MacromoleculeName: Internal virion protein gp14 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 20.990842 KDa
SequenceString: MCWAAAIPIA ISGAQAISGQ NAQAKMIAAQ TAAGRRQAME IMRQTNIQNA DLSLQARSKL EEASAELTSQ NMQKVQAIGS IRAAIGESM LEGSSMDRIK RVTEGQFIRE ANMVTENYRR DYQAIFAQQL GGTQSAASQI DEIYKSEQKQ KSKLQMVLDP L AIMGSSAA ...String:
MCWAAAIPIA ISGAQAISGQ NAQAKMIAAQ TAAGRRQAME IMRQTNIQNA DLSLQARSKL EEASAELTSQ NMQKVQAIGS IRAAIGESM LEGSSMDRIK RVTEGQFIRE ANMVTENYRR DYQAIFAQQL GGTQSAASQI DEIYKSEQKQ KSKLQMVLDP L AIMGSSAA SAYASGAFDS KSTTKAPIVA AKGTKTGR

UniProtKB: Internal virion protein gp14

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Macromolecule #3: Internal virion protein gp15

MacromoleculeName: Internal virion protein gp15 / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 84.454008 KDa
SequenceString: MSKIESALQA AQPGLSRLRG GAGGMGYRAA TTQAEQPRSS LLDTIGRFAK AGADMYTAKE QRARDLADER SNEIIRKLTP EQRREALNN GTLLYQDDPY AMEALRVKTG RNAAYLVDDD VMQKIKEGVF RTREEMEEYR HSRLQEGAKV YAEQFGIDPE D VDYQRGFN ...String:
MSKIESALQA AQPGLSRLRG GAGGMGYRAA TTQAEQPRSS LLDTIGRFAK AGADMYTAKE QRARDLADER SNEIIRKLTP EQRREALNN GTLLYQDDPY AMEALRVKTG RNAAYLVDDD VMQKIKEGVF RTREEMEEYR HSRLQEGAKV YAEQFGIDPE D VDYQRGFN GDITERNISL YGAHDNFLSQ QAQKGAIMNS RVELNGVLQD PDMLRRPDSA DFFEKYIDNG LVTGAIPSDA QA TQLISQA FSDASSRAGG ADFLMRVGDK KVTLNGATTT YRELIGEEQW NALMVTAQRS QFETDAKLNE QYRLKINSAL NQE DPRTAW EMLQGIKAEL DKVQPDEQMT PQREWLISAQ EQVQNQMNAW TKAQAKALDD SMKSMNKLDV IDKQFQKRIN GEWV STDFK DMPVNENTGE FKHSDMVNYA NKKLAEIDSM DIPDGAKDAM KLKYLQADSK DGAFRTAIGT MVTDAGQEWS AAVIN GKLP ERTPAMDALR RIRNADPQLI AALYPDQAEL FLTMDMMDKQ GIDPQVILDA DRLTVKRSKE QRFEDDKAFE SALNAS KAP EIARMPASLR ESARKIYDSV KYRSGNESMA MEQMTKFLKE STYTFTGDDV DGDTVGVIPK NMMQVNSDPK SWEQGRD IL EEARKGIIAS NPWITNKQLT MYSQGDSIYL MDTTGQVRVR YDKELLSKVW SENQKKLEEK AREKALADVN KRAPIVAA T KAREAAAKRV REKRKQTPKF IYGRKE

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Macromolecule #4: Peptidoglycan transglycosylase gp16

MacromoleculeName: Peptidoglycan transglycosylase gp16 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
EC number: Lyases; Carbon-oxygen lyases; Acting on polysaccharides
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 144.028219 KDa
SequenceString: MDKYDKNVPS DYDGLFQKAA DANGVSYDLL RKVAWTESRF VPTAKSKTGP LGMMQFTKAT AKALGLRVTD GPDDDRLNPE LAINAAAKQ LAGLVGKFDG DELKAALAYN QGEGRLGNPQ LEAYSKGDFA SISEEGRNYM RNLLDVAKSP MAGQLETFGG I TPKGKGIP ...String:
MDKYDKNVPS DYDGLFQKAA DANGVSYDLL RKVAWTESRF VPTAKSKTGP LGMMQFTKAT AKALGLRVTD GPDDDRLNPE LAINAAAKQ LAGLVGKFDG DELKAALAYN QGEGRLGNPQ LEAYSKGDFA SISEEGRNYM RNLLDVAKSP MAGQLETFGG I TPKGKGIP AEVGLAGIGH KQKVTQELPE STSFDVKGIE QEATAKPFAK DFWETHGETL DEYNSRSTFF GFKNAAEAEL SN SVAGMAF RAGRLDNGFD VFKDTITPTR WNSHIWTPEE LEKIRTEVKN PAYINVVTGG SPENLDDLIK LANENFENDS RAA EAGLGA KLSAGIIGAG VDPLSYVPMV GVTGKGFKLI NKALVVGAES AALNVASEGL RTSVAGGDAD YAGAALGGFV FGAG MSAIS DAVAAGLKRS KPEAEFDNEF IGPMMRLEAR ETARNANSAD LSRMNTENMK FEGEHNGVPY EDLPTERGAV VLHDG SVLS ASNPINPKTL KEFSEVDPEK AARGIKLAGF TEIGLKTLGS DDADIRRVAI DLVRSPTGMQ SGASGKFGAT ASDIHE RLH GTDQRTYNDL YKAMSDAMKD PEFSTGGAKM SREETRYTIY RRAALAIERP ELQKALTPSE RIVMDIIKRH FDTKREL ME NPAIFGNTKA VSIFPESRHK GTYVPHVYDR HAKALMIQRY GAEGLQEGIA RSWMNSYVSR PEVKARVDEM LKELHGVK E VTPEMVEKYA MDKAYGISHS DQFTNSSIIE ENIEGLVGIE NNSFLEARNL FDSDLSITMP DGQQFSVNDL RDFDMFRIM PAYDRRVNGD IAIMGSTGKT TKELKDEILA LKAKAEGDGK KTGEVHALMD TVKILTGRAR RNQDTVWETS LRAINDLGFF AKNAYMGAQ NITEIAGMIV TGNVRALGHG IPILRDTLYK SKPVSAKELK ELHASLFGKE VDQLIRPKRA DIVQRLREAT D TGPAVANI VGTLKYSTQE LAARSPWTKL LNGTTNYLLD AARQGMLGDV ISATLTGKTT RWEKEGFLRG ASVTPEQMAG IK SLIKEHM VRGEDGKFTV KDKQAFSMDP RAMDLWRLAD KVADEAMLRP HKVSLQDSHA FGALGKMVMQ FKSFTIKSLN SKF LRTFYD GYKNNRAIDA ALSIITSMGL AGGFYAMAAH VKAYALPKEK RKEYLERALD PTMIAHAALS RSSQLGAPLA MVDL VGGVL GFESSKMARS TILPKDTVKE RDPNKPYTSR EVMGAMGSNL LEQMPSAGFV ANVGATLMNA AGVVNSPNKA TEQDF MTGL MNSTKELVPN DPLTQQLVLK IYEANGVNLR ERRK

UniProtKB: Peptidoglycan transglycosylase gp16

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45731
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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