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- EMDB-28562: Focused reconstruction of HRP29 tail -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-28562
TitleFocused reconstruction of HRP29 tail
Map data
Sample
  • Virus: Shigella phage Buco (virus)
    • Protein or peptide: Gp35
    • Protein or peptide: Gp39CD154
    • Protein or peptide: Gp40
    • Protein or peptide: Gp44
KeywordsHRP29 / VIRUS
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, short tail mechanism / outer membrane / virion component
Similarity search - Function
Tail tubular protein Gp11 / Tail tubular protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin
Similarity search - Domain/homology
Head-tail connector protein / Putative tail protein / Putative tail protein / Putative tail protein
Similarity search - Component
Biological speciesShigella phage Buco (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSubramanian S / Bergland Drarvik SM / Parent KN
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
CitationJournal: To Be Published
Title: Structure of Shigella bacteriophage HRP29
Authors: Subramanian S / Bergland Drarvik SM / Parent KN
History
DepositionOct 13, 2022-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28562.png

Downloads & links

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Map

FileDownload / File: emd_28562.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.632 Å
Density
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.07160849 - 0.14511022
Average (Standard dev.)0.00014121381 (±0.0033292621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-189-189-189
Dimensions380380380
Spacing380380380
CellA=B=C: 620.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28562_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28562_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28562_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 : Shigella phage Buco

EntireName: Shigella phage Buco (virus)
Components
  • Virus: Shigella phage Buco (virus)
    • Protein or peptide: Gp35
    • Protein or peptide: Gp39CD154
    • Protein or peptide: Gp40
    • Protein or peptide: Gp44

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Supramolecule #1: Shigella phage Buco

SupramoleculeName: Shigella phage Buco / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2530183 / Sci species name: Shigella phage Buco / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Gp35

MacromoleculeName: Gp35 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Buco (virus)
Molecular weightTheoretical: 56.983391 KDa
SequenceString: MQGQQKESLE SLFTKDSDPT VLDAAEQFAQ WTLPTVLTRD ISGMDGKRTS LHRDYQSTGA VLVNSASTKV TNALFPQGAP FFRFVDSPD MAAAVAELGI NGTVQSQQSQ IELSASSLVF SRDNYAASLR AVKLLMVTGN ALEYFDEGTG RSHIYSVREY T VRRDGSGN ...String:
MQGQQKESLE SLFTKDSDPT VLDAAEQFAQ WTLPTVLTRD ISGMDGKRTS LHRDYQSTGA VLVNSASTKV TNALFPQGAP FFRFVDSPD MAAAVAELGI NGTVQSQQSQ IELSASSLVF SRDNYAASLR AVKLLMVTGN ALEYFDEGTG RSHIYSVREY T VRRDGSGN ILRVVLKERI AAMDLPQEFR SAHLGQKDDY DDVTLYTGIC LEDNKFKIYQ EVQQQQIGDA STYPIDECPY TV LVWNLVN GEHYGRGLVE DYAGDFARLS VLSQALTLYE VEAARLYNAV SAGAGIDVDA AQAAETGDYV QTSAAPGTNP GIW AVENGS DRKIMSLQSE ISMIEQKLAR AFMYAGNTRQ GERVTAYEIR TNAQEAQNSL GDAYSILSDH WLRKRAYLYT VYQY PPMRA MFTLGATTIQ ILVGTASLNK AAQADRLLEA SQSIQLVLPV LQGATKRTNP DAVVDFILDA FGVVSSKLMY TEEQL KQIQ DQQDQQQADQ QRNLELAQAN PEVAGQQLGL IPS

UniProtKB: Head-tail connector protein

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Macromolecule #2: Gp39

MacromoleculeName: Gp39 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Buco (virus)
Molecular weightTheoretical: 20.81551 KDa
SequenceString:
MRLTDAVNVT LEALGESRIV DINTSNPSAG LARAALDRTR RGVLSTGWWF NTIIREVTPT PNPGQIKVPW NQLSMYGLDG TKYGERDGV LYNLVDQTKV FSDTVHLKVV IDIDFEDLPE HMAMWVANAT AAQVYLNDLG ADGNYKSLLG IAAEYEAMNM R EHLRNQRY STSRTHAARK IRSGFFR

UniProtKB: Putative tail protein

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Macromolecule #3: Gp40

MacromoleculeName: Gp40 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Buco (virus)
Molecular weightTheoretical: 84.783617 KDa
SequenceString: MAQTFEGTLQ SLLQGVSQQI PRERQPGQLG AQQNMLSDPV TGLRRRPPLH LAAQTLMENP VSPDALFSTY IERGTDGRHL LINTEAGIW QILSKDATTL IRSGQADYLK ASIGATSIQT ASIAGLTYIL NTEQTPVAHV DNTGKLNPAN TGFFYIVASS F SKRWTITV ...String:
MAQTFEGTLQ SLLQGVSQQI PRERQPGQLG AQQNMLSDPV TGLRRRPPLH LAAQTLMENP VSPDALFSTY IERGTDGRHL LINTEAGIW QILSKDATTL IRSGQADYLK ASIGATSIQT ASIAGLTYIL NTEQTPVAHV DNTGKLNPAN TGFFYIVASS F SKRWTITV QSNEGTWTAV HDVGASSDDG AVPAATASAV INSLKTNLLA AGMPSDKVDT FGSYMFIKGL TNVVVSSDAG TT YARWSNQ SRVDEESDLP AQLPASANGC MCRVGAASTS ATWYRFDYAT RQWNEDSAYS SITKITNMPL EFAADDQIIP RDF EGRLAG DDENNEDPGF VENGYITGIA AFQGRLVLLS GSRVSMSASG LYQRFYRSTV VNLLDTDRID IGAASAQDSV FRAA LQFNR DLVVFGDSMQ AVIAGNAVLT PTNASIALTS EFSCDSRVIP VVTGQTVLYA SRRNSDYAGL LEFIPSAYTS SQYVS QDAT VHLPRYIPGR VMDMQVSSVT NVAFFRYSGE RTSVLVYEFL WGEDAKRAQG AYHKWVLPYD VLSLHTLSEA AYFFVR GPG AYVLALRVDP REGFVAGTTY EYPFMDMGAP VTVQGGQFTL PEHLRKAGLQ DSIALAYYTG DDSGSELGIA SISSNWV CT TVRGVPDGNY LAGYRFKSGT TLTPPMLKDQ NDNLIGSGHV RLLRLDVAMR NSGVVDVLVE DNARDVDNDS EYSGVLMN S KELAPEQPLK ASLSNIIIPC RTNTDTTEVT LSTSGTLEMN IMDVSYILRY NQRRRRV

UniProtKB: Putative tail protein

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Macromolecule #4: Gp44

MacromoleculeName: Gp44 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Buco (virus)
Molecular weightTheoretical: 28.595883 KDa
SequenceString: MAYSWSEQVV PSGTTLISVD IEYLDKSYIY LYINNVLISN SDYSWNSDTL IQLNTPMASA GTVLLVRRTD KEYLYIMFAE GAAFIRENL DVQNTQFLHL AQELVEGRSI DGFYGDLSMN GYRITHLADG VDPKDAVNKG QLDSVSNRVS SIENSFLGLT T VSYPWYTV ...String:
MAYSWSEQVV PSGTTLISVD IEYLDKSYIY LYINNVLISN SDYSWNSDTL IQLNTPMASA GTVLLVRRTD KEYLYIMFAE GAAFIRENL DVQNTQFLHL AQELVEGRSI DGFYGDLSMN GYRITHLADG VDPKDAVNKG QLDSVSNRVS SIENSFLGLT T VSYPWYTV VSADTDTFEP PFKFTKAALY IDGLCQVPDY SYVVVDNKLL LAESVPTGTV VFARLGEDTD AATEAATTTA LA AVQADLQ NQINALRALL QGG

UniProtKB: Putative tail 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: 7.5
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: 3.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 33.0 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24391
FSC plot (resolution estimation)

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