[English] 日本語
Yorodumi
- EMDB-71729: PhuZ Tubulin from phage Goslar (locally refined monomer) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71729
TitlePhuZ Tubulin from phage Goslar (locally refined monomer)
Map data
Sample
  • Organelle or cellular component: Tubulin PhuZ from Bacteriophage Goslar
    • Protein or peptide: Tubulin/FtsZ GTPase domain-containing protein
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
KeywordsPhage / Tubulin / PhuZ / VIRAL PROTEIN
Function / homologyTubulin/FtsZ, GTPase domain superfamily / Tubulin/FtsZ GTPase domain-containing protein
Function and homology information
Biological speciesGoslarvirus
Methodhelical reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsBasu D / Gu Y / Corbett KD
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: Structure / Year: 2026
Title: A bacteriophage tubulin forms microtubule-like assemblies with nine protofilaments.
Authors: Dwaipayan Basu / Siyu Chen / Ying-Xing Li / Niklas Klusch / Koe Inlow / Joe Pogliano / Elizabeth Villa / Kevin D Corbett /
Abstract: Tubulin family proteins play central roles in the organization and dynamics of cytoskeletal systems across the Tree of Life. In one family of bacteriophages (phages), tubulin-like proteins called ...Tubulin family proteins play central roles in the organization and dynamics of cytoskeletal systems across the Tree of Life. In one family of bacteriophages (phages), tubulin-like proteins called PhuZ (Phage tubulin/FtsZ) form dynamic filaments that position and rotate an intracellular compartment, the "phage nucleus," in which the phage genome is replicated. PhuZ filaments also mediate trafficking of nascent capsids from the cell periphery to the phage nucleus for genome packaging. PhuZ from the Pseudomonas-infecting phages 201Phi2-1 and PhiKZ form assemblies with three protofilaments. Here, we determine a 2.8 Å resolution structure of PhuZ from the E. coli-infecting phage Goslar, which forms an elaborate "cytoskeletal vortex" in infected cells. We find that in vitro-assembled Goslar PhuZ forms rigid tubes with nine nearly-straight protofilaments. The lateral interactions mediating this assembly are fundamentally different from eukaryotic tubulin, leading to a distinctive overall architecture for Goslar PhuZ filaments.
History
DepositionJul 16, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71729.png

Downloads & links

-
Map

FileDownload / File: emd_71729.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.)
0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.3478667 - 0.7707536
Average (Standard dev.)0.0029601038 (±0.017432993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_71729_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_71729_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tubulin PhuZ from Bacteriophage Goslar

EntireName: Tubulin PhuZ from Bacteriophage Goslar
Components
  • Organelle or cellular component: Tubulin PhuZ from Bacteriophage Goslar
    • Protein or peptide: Tubulin/FtsZ GTPase domain-containing protein
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

-
Supramolecule #1: Tubulin PhuZ from Bacteriophage Goslar

SupramoleculeName: Tubulin PhuZ from Bacteriophage Goslar / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Goslarvirus

-
Macromolecule #1: Tubulin/FtsZ GTPase domain-containing protein

MacromoleculeName: Tubulin/FtsZ GTPase domain-containing protein / type: protein_or_peptide / ID: 1 / Details: Codon 1 deleted; N-terminal SNA tag scar / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Goslarvirus
Molecular weightTheoretical: 35.662961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAQENQVHI WAVGGCGGEI GSAFEGEVAK GLHSMTYVDT SRANLRDSTL GDDHIYIFKD AAGRELDGSG KKRDENAELI CSQIPGILN KHTPGKFNIV VFSLSGGSGS VAGPALVANL LERGERVVCC IVASFDDERQ TINADRTFKG LMAAAEGLKR P VIVSYHMN ...String:
SNAQENQVHI WAVGGCGGEI GSAFEGEVAK GLHSMTYVDT SRANLRDSTL GDDHIYIFKD AAGRELDGSG KKRDENAELI CSQIPGILN KHTPGKFNIV VFSLSGGSGS VAGPALVANL LERGERVVCC IVASFDDERQ TINADRTFKG LMAAAEGLKR P VIVSYHMN GENGKSEQDV NLDVQVVISQ LCVLFSGENR RLDSADLENF LNHPRVTGLE PTITELNTFM GYEWTKENDS PI AFCTLYP KDATKVMGVS AIYSCDGFVP ESSPIREATS FVLSTDRLGG IIKQIADEAK RYIEHRNARQ QAPKVGDETV AEA KNSGFL LF

UniProtKB: Tubulin/FtsZ GTPase domain-containing protein

-
Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 2 / Number of copies: 1 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.883 Å
Applied symmetry - Helical parameters - Δ&Phi: -79.906 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 396117
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
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