[English] 日本語
Yorodumi
- EMDB-44517: Pseudomonas phage DEV neck and tail (portal, head-to-tail and tai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44517
TitlePseudomonas phage DEV neck and tail (portal, head-to-tail and tail tube proteins)
Map data
Sample
  • Complex: Portal to tail complex of Pseudomonas phage DEV
    • Protein or peptide: gp75 tail tube
    • Protein or peptide: gp83 head-to-tail
    • Protein or peptide: gp80 portal protein
Keywordsportal / tail hub / tail tube / complex / STRUCTURAL PROTEIN / gp75 / gp83 / gp80 / VIRAL PROTEIN
Function / homologyTail protein / N4 gp54-like protein / Portal protein
Function and homology information
Biological speciesPseudomonas phage vB_PaeP_DEV (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsIglesias SM / Hou CFD / Li F / Cingolani G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
CitationJournal: To Be Published
Title: Integrative structural analysis of Pseudomonas phage DEV reveals a genome ejection motor
Authors: Lokareddy R / Hou C-FD / Forti F / Iglesias SM / Li F / Pavlenok M / Niederweis M / Briani F / Cingolani G
History
DepositionApr 19, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44517.png

Downloads & links

-
Map

FileDownload / File: emd_44517.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.01572903 - 0.052771408
Average (Standard dev.)-0.00027810902 (±0.0027997014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 573.44 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_44517_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_44517_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_44517_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Portal to tail complex of Pseudomonas phage DEV

EntireName: Portal to tail complex of Pseudomonas phage DEV
Components
  • Complex: Portal to tail complex of Pseudomonas phage DEV
    • Protein or peptide: gp75 tail tube
    • Protein or peptide: gp83 head-to-tail
    • Protein or peptide: gp80 portal protein

-
Supramolecule #1: Portal to tail complex of Pseudomonas phage DEV

SupramoleculeName: Portal to tail complex of Pseudomonas phage DEV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)

-
Macromolecule #1: gp75 tail tube

MacromoleculeName: gp75 tail tube / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 35.267215 KDa
SequenceString: MAVEPITIAD LTEVKLDGKG ALDQLLQVTR LHLAKEHDAG RLKGQEYAAV LTGGITAVLQ NAVMFLLQKD EAANKAALVE AQIKLTEKQ GELLDKQIAQ ADKDAELIAA KVKLTLEQAK LPDSQIRSAG FQDLLVQEQT KVQTAQTRRI DQEILSAGFQ D LLVKEQTA ...String:
MAVEPITIAD LTEVKLDGKG ALDQLLQVTR LHLAKEHDAG RLKGQEYAAV LTGGITAVLQ NAVMFLLQKD EAANKAALVE AQIKLTEKQ GELLDKQIAQ ADKDAELIAA KVKLTLEQAK LPDSQIRSAG FQDLLVQEQT KVQTAQTRRI DQEILSAGFQ D LLVKEQTA KTKQDVLTAV QQTKVMEQQV LESTQKVLNM KQELLNLVAQ ECLLKAQFDL TKDQGLNTQE QTILVRQKVA SE RAQTIGA GVDADSVIGR QKELYKAQAD GFKRDAEQKA AKILIDTWNV RRTTDTGTQA NTTNRLDDAN VGRVVNMLMT GVG A

UniProtKB: N4 gp54-like protein

-
Macromolecule #2: gp83 head-to-tail

MacromoleculeName: gp83 head-to-tail / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 27.868934 KDa
SequenceString: MTIQLKQVID LLAEGELSNI KYVNIDTGAL VLERVPSLIR AINLGVLDLH KRFLLKEGML KIQLEEGRRL YPLRPAYQVG QKPKPGVPQ FITEGNKLGR QSILKIEKII GDNGVEYYLN DTWQPLNITT PEFDVLEISD EFYCHSSSKT LEVRYRRAPT P MKICVDNL ...String:
MTIQLKQVID LLAEGELSNI KYVNIDTGAL VLERVPSLIR AINLGVLDLH KRFLLKEGML KIQLEEGRRL YPLRPAYQVG QKPKPGVPQ FITEGNKLGR QSILKIEKII GDNGVEYYLN DTWQPLNITT PEFDVLEISD EFYCHSSSKT LEVRYRRAPT P MKICVDNL DSWGCIDIDL PYTHLQALLY FVASRCQTPI GFMENTAQEG FNFSQKYEAE CANLDAQNLR IDPVGNQDRF TR GGWV

UniProtKB: Tail protein

-
Macromolecule #3: gp80 portal protein

MacromoleculeName: gp80 portal protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 81.739453 KDa
SequenceString: MADVDEDYLT LPNEDGDPSK RLQPEWSNAP SLAQLKQDYQ EAKQVTDEKI TQINRWLDYM HVRGEGKPKT EKGKSAVQPP TIRKQAEWR YSSLSEPFLS SPNIFEVNPV TWEDAESARQ NGLVLNQQFN TKLNKQRFID EYVRAGVDEG TIIVKVGWNY Q SRTVKEQV ...String:
MADVDEDYLT LPNEDGDPSK RLQPEWSNAP SLAQLKQDYQ EAKQVTDEKI TQINRWLDYM HVRGEGKPKT EKGKSAVQPP TIRKQAEWR YSSLSEPFLS SPNIFEVNPV TWEDAESARQ NGLVLNQQFN TKLNKQRFID EYVRAGVDEG TIIVKVGWNY Q SRTVKEQV VTYEMMPDSS EELAQIYQTA AQIREESPSE YPEIPEDVRL GLEETEANGI QVRAVPVGSE EEEREETVEN HP TVQVCDY NNIVIDPSCG SDFSKAKFLI ETFESSYAEL KADGRYKNLD KIQVEGQNLL SEPDYTGPSE GVRNFDFQDK SRK RLVVHE YWGYYDIHGD GVLHPIVATW VGAVMIRMEE NPFPDKKIPY VVVSYIPRKR DLYGESDGAL LIDNQRIIGA VTRG MIDTM ARSANGQVGV MKGALDVTNR RRFDRGENYE FNPGADPRAA VHMHTFPEIP QSAQYMINLQ QAEAESMTGV KAFNA GISG AALGDTATAV RGALDAASKR ELGILRRLSA GIIEIGRKII AMNAEFLDDV EVVRITNEHF VDIRRDDLAG NFDLKL DIS TAEEDNAKVN DLTFMLQTMG PNMDPMMAQQ IMGQIMELKK MPDFAKRIRE FQPQPDPIAQ QKAQLELMLL QAQIEAE RA RAAHYMSGAG LQDSKVGTEQ AKARALASQA DMTDLNFLEQ ESGVQQARKR ELQQAQSEAQ GKLAMLNSQL KRLDEATS A RTSQK

UniProtKB: Portal protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3228
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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://pdbjlvh1.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