[English] 日本語
Yorodumi
- EMDB-35826: Tail fiber of phage lambda tail -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35826
TitleTail fiber of phage lambda tail
Map data
Sample
  • Complex: Tail tip conformation 1 of phage lambda tail
    • Protein or peptide: gpJ
KeywordsBacteriophage / caudovirales / siphoviridae / tail complex / delivery device / macromolecular assembly / phage lambda / cryo-EM / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / receptor-mediated virion attachment to host cell / virion attachment to host cell
Similarity search - Function
Domain of unknown function DUF3672 / : / Tip attachment protein J, C-terminal receptor binding domain / Tip attachment protein J, Ig-like domain / Tip attachment protein J second Ig-like domain / Domain of unknown function DUF1983 / : / : / Bacteriophage tail tip fiber protein / Tip attachment protein J,FNIII-A domain ...Domain of unknown function DUF3672 / : / Tip attachment protein J, C-terminal receptor binding domain / Tip attachment protein J, Ig-like domain / Tip attachment protein J second Ig-like domain / Domain of unknown function DUF1983 / : / : / Bacteriophage tail tip fiber protein / Tip attachment protein J,FNIII-A domain / Tip attachment protein J / Putative phage tail protein / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tip attachment protein J
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.07 Å
AuthorsWang JW / Wang C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Structure / Year: 2024
Title: Architecture of the bacteriophage lambda tail.
Authors: Chang Wang / Jinsong Duan / Zhiwei Gu / Xiaofei Ge / Jianwei Zeng / Jiawei Wang /
Abstract: Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host ...Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host recognition and delivery of viral DNA from the head shell to the cytoplasm of the infected cell. Here, we present a high-resolution structure of the tail complex of bacteriophage lambda determined by cryoelectron microscopy. Most component proteins of the lambda tail were determined at the atomic scale. The structure sheds light on the molecular organization of the extensively studied tail of bacteriophage lambda.
History
DepositionApr 5, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_35826.png

Downloads & links

-
Map

FileDownload / File: emd_35826.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 429.68 Å		1.07 Å/pix.
x 400 pix.
= 429.68 Å		1.07 Å/pix.
x 400 pix.
= 429.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.365
Minimum - Maximum-0.9498841 - 1.9078748
Average (Standard dev.)-0.0023901486 (±0.033707995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 429.68002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half 1 map

Fileemd_35826_half_map_1.map
Annotationhalf 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half 2 map

Fileemd_35826_half_map_2.map
Annotationhalf 2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tail tip conformation 1 of phage lambda tail

EntireName: Tail tip conformation 1 of phage lambda tail
Components
  • Complex: Tail tip conformation 1 of phage lambda tail
    • Protein or peptide: gpJ

-
Supramolecule #1: Tail tip conformation 1 of phage lambda tail

SupramoleculeName: Tail tip conformation 1 of phage lambda tail / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage Lambda (virus)

-
Macromolecule #1: gpJ

MacromoleculeName: gpJ / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
SequenceString: MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETVL GTEVKYDTPI TRTITSANID RLRFTFGVQA LVETTSKGDR NPSEVRLLVQ IQRNGGWVTE KDITIKGKTT SQYLASVVMG ...String:
MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETVL GTEVKYDTPI TRTITSANID RLRFTFGVQA LVETTSKGDR NPSEVRLLVQ IQRNGGWVTE KDITIKGKTT SQYLASVVMG NLPPRPFNIR MRRMTPDSTT DQLQNKTLWS SYTEIIDVKQ CYPNTALVGV QVDSEQFGSQ QVSRNYHLRG RILQVPSNYN PQTRQYSGIW DGTFKPAYSN NMAWCLWDML THPRYGMGKR LGAADVDKWA LYVIGQYCDQ SVPDGFGGTE PRITCNAYLT TQRKAWDVLS DFCSAMRCMP VWNGQTLTFV QDRPSDKTWT YNRSNVVMPD DGAPFRYSFS ALKDRHNAVE VNWIDPNNGW ETATELVEDT QAIARYGRNV TKMDAFGCTS RGQAHRAGLW LIKTELLETQ TVDFSVGAEG LRHVPGDVIE ICDDDYAGIS TGGRVLAVNS QTRTLTLDRE ITLPSSGTAL ISLVDGSGNP VSVEVQSVTD GVKVKVSRVP DGVAEYSVWE LKLPTLRQRL FRCVSIREND DGTYAITAVQ HVPEKEAIVD NGAHFDGEQS GTVNGVTPPA VQHLTAEVTA DSGEYQVLAR WDTPKVVKGV SFLLRLTVTA DDGSERLVST ARTTETTYRF TQLALGNYRL TVRAVNAWGQ QGDPASVSFR IAAPAAPSRI ELTPGYFQIT ATPHLAVYDP TVQFEFWFSE KQIADIRQVE TSTRYLGTAL YWIAASINIK PGHDYYFYIR SVNTVGKSAF VEAVGRASDD AEGYLDFFKG KITESHLGKE LLEKVELTED NASRLEEFSK EWKDASDKWN AMWAVKIEQT KDGKHYVAGI GLSMEDTEEG KLSQFLVAAN RIAFIDPANG NETPMFVAQG NQIFMNDVFL KRLTAPTITS GGNPPAFSLT PDGKLTAKNA DISGSVNANS GTLSNVTIAE NCTINGTLRA EKIVGDIVKA ASAAFPRQRE SSVDWPSGTR TVTVTDDHPF DRQIVVLPLT FRGSKRTVSG RTTYSMCYLK VLMNGAVIYD GAANEAVQVF SRIVDMPAGR GNVILTFTLT STRHSADIPP YTFASDVQVM VIKKQALGIS VV

UniProtKB: Tip attachment protein J

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

-
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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28128
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://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