[English] 日本語
Yorodumi
- PDB-9e7m: In situ cryoEM structure of bacteriophage Ur-lambda tail tip complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e7m
TitleIn situ cryoEM structure of bacteriophage Ur-lambda tail tip complex
Components
  • (Tail tip assembly protein ...) x 2
  • (Tail tip protein ...) x 2
  • Tail fiber protein
  • Tail tube protein
  • Tape measure protein
  • Tip attachment protein J
KeywordsVIRAL PROTEIN / bacteriophage / tail tip complex
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, fiber / viral tail assembly / virus tail / adhesion receptor-mediated virion attachment to host cell / 4 iron, 4 sulfur cluster binding / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell ...virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, fiber / viral tail assembly / virus tail / adhesion receptor-mediated virion attachment to host cell / 4 iron, 4 sulfur cluster binding / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Lambda-like tail fibre protein, N-terminal / Prophage tail fibre N-terminal / Bacteriophage lambda, Tail fiber protein, repeat-1 / Phage tail fibre repeat / Bacteriophage lambda, Tail fiber protein, repeat-2 / Phage tail fibre repeat / Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein ...Lambda-like tail fibre protein, N-terminal / Prophage tail fibre N-terminal / Bacteriophage lambda, Tail fiber protein, repeat-1 / Phage tail fibre repeat / Bacteriophage lambda, Tail fiber protein, repeat-2 / Phage tail fibre repeat / Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Phage minor tail protein L / Phage minor tail protein / Bacteriophage lambda tail assembly protein I / Phage tail collar domain superfamily / Phage tail collar domain / : / Phage Tail Collar 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 / : / : / Tip attachment protein J,FNIII-A domain / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Tip attachment protein J / Putative phage tail protein / Carboxypeptidase-like, regulatory domain superfamily / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Beta-grasp domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Tail tip assembly protein I / Tail tube protein / Tape measure protein / Tail tip protein M / Tail tip protein L / Tip attachment protein J / Tail fiber protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsYu, H. / Liu, J. / Molineux, I.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)110243 United States
CitationJournal: To Be Published
Title: Structural basis of bacteriophage Ur-lambda infection initiation
Authors: Yu, H. / Liu, J. / Molineux, I.J.
History
DepositionNov 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 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
Ha: Tape measure protein
Ia: Tail tip assembly protein I
Hb: Tape measure protein
Ib: Tail tip assembly protein I
Hc: Tape measure protein
Ic: Tail tip assembly protein I
Ja: Tip attachment protein J
Jb: Tip attachment protein J
Jc: Tip attachment protein J
Lc: Tail tip protein L
Lb: Tail tip protein L
La: Tail tip protein L
Ta: Tail fiber protein
Tb: Tail fiber protein
Tc: Tail fiber protein
Td: Tail fiber protein
Te: Tail fiber protein
Tf: Tail fiber protein
Tg: Tail fiber protein
Tl: Tail fiber protein
Th: Tail fiber protein
Ti: Tail fiber protein
Tj: Tail fiber protein
Tk: Tail fiber protein
Ma: Tail tip protein M
Mb: Tail tip protein M
Mc: Tail tip protein M
Md: Tail tip protein M
Me: Tail tip protein M
Mf: Tail tip protein M
Va: Tail tube protein
Vb: Tail tube protein
Vc: Tail tube protein
Vd: Tail tube protein
Ve: Tail tube protein
Vf: Tail tube protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)689,33639
Polymers688,28136
Non-polymers1,0553
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Tail tip assembly protein ... , 2 types, 3 molecules IaIbIc

#2: Protein Tail tip assembly protein I


Mass: 9322.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: I, lambdap20 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03730
#3: Protein Tail tip assembly protein I


Mass: 9308.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: I, lambdap20 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03730

-
Protein , 3 types, 21 molecules JaJbJcTaTbTcTdTeTfTgTlThTiTjTkVaVbVcVdVeVf

#4: Protein Tip attachment protein J / Central tail fiber / Host specificity protein J


Mass: 92362.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: J, lambdap21 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03749
#6: Protein
Tail fiber protein / stf / Gene product 27 / gp27


Mass: 10092.285 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: stf, lambdap27 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03764
#8: Protein
Tail tube protein / TTP / Gene product V / gpV / Major tail protein V


Mass: 16540.227 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: V, lambdap13 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03733

-
Tail tip protein ... , 2 types, 9 molecules LcLbLaMaMbMcMdMeMf

#5: Protein Tail tip protein L


Mass: 25730.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: L, lambdap18 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03738
#7: Protein
Tail tip protein M


Mass: 12547.373 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: M, lambdap17 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03737

-
Protein/peptide / Non-polymers , 2 types, 6 molecules HaHbHc

#1: Protein/peptide Tape measure protein / TMP / Gene product H / gpH / Minor tail protein H


Mass: 3471.985 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: H, lambdap16 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03736
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Escherichia phage Ur-lambda / Type: VIRUS / Entity ID: #1-#8 / Source: NATURAL
Source (natural)Organism: Escherichia phage Ur-lambda (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.6
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: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.21_5190 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6517 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 94.58 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003549272
ELECTRON MICROSCOPYf_angle_d0.659867023
ELECTRON MICROSCOPYf_chiral_restr0.04437493
ELECTRON MICROSCOPYf_plane_restr0.00448744
ELECTRON MICROSCOPYf_dihedral_angle_d4.84466811

+
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