[English] 日本語
Yorodumi
- PDB-9efk: Cryo-EM structure of the portal-tail complex of LME-1 phage -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9efk
TitleCryo-EM structure of the portal-tail complex of LME-1 phage
Components
  • orf12
  • orf17
  • orf18
  • orf22
KeywordsVIRAL PROTEIN / LME-1 / legionella pneumophila / phage / portal / tail / podovirus / podophage
Function / homologyHead-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsDeme, J.C. / Lea, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Phage resistance as an unexpected environmental determinant of the accidental virulence of Legionella pneumophila against the human host.
Authors: Nicholson, B. / Sante, J.F. / Chaney, E.H. / Deme, J.C. / Deecker, S.R. / Sztanko, K. / Davidson, A.R. / Lea, S.M. / Ensminger, A.W.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: orf12
M: orf18
N: orf18
O: orf18
P: orf18
Q: orf18
R: orf18
AE: orf22
AF: orf22
AG: orf22
AN: orf22
AO: orf22
AP: orf22
AW: orf22
AX: orf22
AY: orf22
BF: orf22
BG: orf22
BH: orf22
BO: orf22
BP: orf22
BQ: orf22
BX: orf22
BY: orf22
BZ: orf22
B: orf12
C: orf12
D: orf12
E: orf12
F: orf12
G: orf12
H: orf12
I: orf12
J: orf12
K: orf12
L: orf12
T: orf17
AC: orf17
AD: orf17
S: orf17
X: orf17
U: orf17
V: orf17
W: orf17
Y: orf17
Z: orf17
AA: orf17
AB: orf17


Theoretical massNumber of molelcules
Total (without water)2,804,71148
Polymers2,804,71148
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
orf12


Mass: 62743.062 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A140AYN0
#2: Protein
orf18


Mass: 89921.969 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A140AYN6
#3: Protein
orf22


Mass: 68819.797 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A140AYP0
#4: Protein
orf17


Mass: 22792.135 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A140AYN5
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: LME-1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: LME-1 (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 52.9 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

-
Processing

EM softwareName: PHENIX / Version: dev_5430 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88530 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 51.88 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047132450
ELECTRON MICROSCOPYf_angle_d0.5187180510
ELECTRON MICROSCOPYf_chiral_restr0.047320358
ELECTRON MICROSCOPYf_plane_restr0.004223562
ELECTRON MICROSCOPYf_dihedral_angle_d12.696548114

+
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