[English] 日本語
Yorodumi
- EMDB-18489: Tail channel of phage 812 virion (C3) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18489
TitleTail channel of phage 812 virion (C3)
Map dataTail channel of phage 812 virion (C3)
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail tape measure protein
Keywordsphage / neck / tail / connector / VIRUS
Function / homologyPhage tail lysozyme / Phage tail lysozyme / Major tail sheath protein / Phage tail lysozyme domain-containing protein / Capsid protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.56 Å
AuthorsCienikova Z / Novacek J / Fuzik T / Benesik M / Plevka P
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
CitationJournal: To Be Published
Title: Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812
Authors: Cienikova Z / Novacek J / Siborova M / Popelarova B / Fuzik T / Benesik M / Bardy P / Plevka P
History
DepositionSep 20, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18489.png

Downloads & links

-
Map

FileDownload / File: emd_18489.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTail channel of phage 812 virion (C3)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 480 pix.
= 518.4 Å		1.08 Å/pix.
x 480 pix.
= 518.4 Å		1.08 Å/pix.
x 480 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.049109932 - 0.056726076
Average (Standard dev.)0.00071227294 (±0.003485649)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18489_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 1

Fileemd_18489_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 2

Fileemd_18489_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Staphylococcus phage 812

EntireName: Staphylococcus phage 812 (virus)
Components
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail tape measure protein

-
Supramolecule #1: Staphylococcus phage 812

SupramoleculeName: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified phage virion / NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Sci species strain: K1-420 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Staphylococcus aureus (bacteria) / Strain: CCM 8428
Virus shellShell ID: 1 / Diameter: 1100.0 Å

-
Macromolecule #1: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 1 / Details: Stacked hexameric rings / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
SequenceString:
MASEAKQTVH TGNTVLLMIK GKPVGRAQSA SGQREYGTTG VYEIGSIMPQ EHVYLRYEGT ITVERLRMKK ENFADLGYAS LGEEILKKDI IDILVVDNLT KQVIISYHGC SANNYNETWQ TNEIVTEEIE FSYLTASDKA RT

UniProtKB: Capsid protein

-
Macromolecule #2: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 2 / Details: Stacked hexameric rings / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
SequenceString: MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILAM RIEDAKPASA EIGGLKITSK IYGNVANNIQ VGLEKNTLSD SLRLRVIFQD DRFNEVYDNI GNIFTIKYKG EEANATFSVE ...String:
MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILAM RIEDAKPASA EIGGLKITSK IYGNVANNIQ VGLEKNTLSD SLRLRVIFQD DRFNEVYDNI GNIFTIKYKG EEANATFSVE HDEETQKASR LVLKVGDQEV KSYDLTGGAY DYTNAIITDI NQLPDFEAKL SPFGDKNLES SKLDKIENAN IKDKAVYVKA VFGDLEKQTA YNGIVSFEQL NAEGEVPSNV EVEAGEESAT VTATSPIKTI EPFELTKLKG GTNGEPPATW ADKLDKFAHE GGYYIVPLSS KQSVHAEVAS FVKERSDAGE PMRAIVGGGF NESKEQLFGR QASLSNPRVS LVANSGTFVM DDGRKNHVPA YMVAVALGGL ASGLEIGESI TFKPLRVSSL DQIYESIDLD ELNENGIISI EFVRNRTNTF FRIVDDVTTF NDKSDPVKAE MAVGEANDFL VSELKVQLED QFIGTRTINT SASIIKDFIQ SYLGRKKRDN EIQDFPAEDV QVIVEGNEAR ISMTVYPIRS FKKISVSLVY KQQTLQA

UniProtKB: Major tail sheath protein

-
Macromolecule #3: Tail tape measure protein

MacromoleculeName: Tail tape measure protein / type: protein_or_peptide / ID: 3 / Details: Trimer occupying the tail tube channel / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus) / Strain: K1-420
SequenceString: MMAMNDDYRL VLSGDSSDLE NSLKAIELYM DSLESKNIDA PLDNFLKKLK VIAKEVKNVQ NAMDKQDGKS VISSKDMDES IKSTQSATKN INELKKALDD LQKENISKGI APDPEVEKAY AKMGKVVDET QEKLEKMSSQ KIGSDASIQN RIKEMKTLNQ VTEEYNKISK ...String:
MMAMNDDYRL VLSGDSSDLE NSLKAIELYM DSLESKNIDA PLDNFLKKLK VIAKEVKNVQ NAMDKQDGKS VISSKDMDES IKSTQSATKN INELKKALDD LQKENISKGI APDPEVEKAY AKMGKVVDET QEKLEKMSSQ KIGSDASIQN RIKEMKTLNQ VTEEYNKISK DSSATKDYTK RLRANRNMTR GYMERSEGTG RLTYDQGARV RSELGKVSSY ESQRKQNQRN LEQAREQYSN YRNQQQDLTK RRASGQINKA QYEQELASIK QEMKAREELI SNYEKLGAEL DKTVQYYKGS VQKDFQSRDV DQQRGTFGRM VQERLPSIGS HAMMGTTAMA TGLYMKGASL SETNRPMVTS LGQNSDNMDI DSVRNAYGDL SIDNKLGYNS TDMLKMATSY EASVGHKSDE DTMAGTKQLA IGGRSLGIKD QEAYQESMGQ IMHTGGVNSD NMKEMQDAFL GGIKQSGMVG RQDEQLKALG SIAEQSGEGR TLTKDQMSNL TAMQSTFAES GSKGLQGEQG ANAINSIDQG LKNGMNSSYA RIAMGWGTQY QGLEGGYDLQ KRMDEGISNP ENLTDMADIA TQMGGSEKEQ KYLFNRSMKE IGANLTMEQS DEIFKDSKEG KLSKEELAKK AKKMEKEGKK EGEDNATDYK ESKSGKNDQN KSKTDDKAED TYDMAQPLRD AHSALAGLPA PIYLAIGAIG AFTASLIASA SQFGAGHLIG KGAKGLRNKF GRNKGGSSGG NPMAGGMPSG GGSPKGGGSP KGGGTRSTGG KILDSAKGLG GFLVGGAGWK GMFGGESKGK GFKQTSKEAW SGTRKVFNRD NGRKAMDKSK DIAKGTGSGL KDIYNDSIFG KERRQNLGEK AKGFGGKAKG LYGKFADKFG DGGKNGILSQ SPKAGGSGIG KLGKLAGGLG KGAGVLGVAT SALSLIPALA SGDSKAIGGG IGSMGGGMAG ASAGASIGAL FGGVGAIPGA LIGGAIGSFG GGAVGEKVGD MAKKANTKEG WNLGWTNGDK DGKNKFQDSL LGKPISKAWS GITGLFDNDA EASEEDSKDK KKGVKGVKGD TKKKEKMTAE QLREKNNQSE TKNLKIYSDL LDRAQKIIES AKGINIDGGT SDSGSDSGGS ASDVGGEGAE KMYKFLKGKG LSDNQVGAVM GNLQQESNLD PNAKNASSGA FGIAQWLGAR KTGLENFAKS KGKKSSDMDV QLDYLWKEMQ SDYESNNLKN AGWSKGGSLE QNTKAFATGF ERMGANEAMM GTRVNNAKEF KKKYGGSGGG GGGGALSSTY QEAMSNPVLT TGSNYRGSND ASNASTTNRI TVNVNVQGGN NPEETGDIIG GRIREVLDSN MDIFANEHKR SY

UniProtKB: Phage tail lysozyme domain-containing protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
10.0 mMNaClsodium chloride
10.0 mMCaClcalcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number real images: 30553 / Average exposure time: 1.0 sec. / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsFrame alignment and dose-weighting with MotionCor2, then contrast inversion and normalization
Particle selectionNumber selected: 23947 / Details: Manual particle selection
Startup modelType of model: EMDB MAP
EMDB ID:

8203

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 13126
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 21722 / Software - Name: RELION (ver. 3.1)
Details: Neck/tail junction reconstructed in C6 was symmetry expanded to C3 then classified with a focused mask on the tail tube channel, without orientation search.
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more