[English] 日本語
Yorodumi
- EMDB-8180: Cryo-EM structure of the MamK filament at 6.5 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8180
TitleCryo-EM structure of the MamK filament at 6.5 A
Map dataNone
Sample
  • Organelle or cellular component: Magnetosome-associated MamK filament
    • Protein or peptide: Actin-like ATPase
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsActin-like / Magnetosome / bacteria / STRUCTURAL PROTEIN
Function / homology
Function and homology information


magnetosome assembly / magnetosome membrane / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cytoskeleton / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
MreB/Mbl protein / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin-like protein MamK
Similarity search - Component
Biological speciesMagnetospirillum magneticum AMB-1 (bacteria) / Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsBergeron JRC / Hutto R
CitationJournal: Protein Sci / Year: 2017
Title: Structure of the magnetosome-associated actin-like MamK filament at subnanometer resolution.
Authors: Julien R C Bergeron / Rachel Hutto / Ertan Ozyamak / Nancy Hom / Jesse Hansen / Olga Draper / Meghan E Byrne / Sepehr Keyhani / Arash Komeili / Justin M Kollman /
Abstract: Magnetotactic bacteria possess cellular compartments called magnetosomes that sense magnetic fields. Alignment of magnetosomes in the bacterial cell is necessary for their function, and this is ...Magnetotactic bacteria possess cellular compartments called magnetosomes that sense magnetic fields. Alignment of magnetosomes in the bacterial cell is necessary for their function, and this is achieved through anchoring of magnetosomes to filaments composed of the protein MamK. MamK is an actin homolog that polymerizes upon ATP binding. Here, we report the structure of the MamK filament at ∼6.5 Å, obtained by cryo-Electron Microscopy. This structure confirms our previously reported double-stranded, nonstaggered architecture, and reveals the molecular basis for filament formation. While MamK is closest in sequence to the bacterial actin MreB, the longitudinal contacts along each MamK strand most closely resemble those of eukaryotic actin. In contrast, the cross-strand interface, with a surprisingly limited set of contacts, is novel among actin homologs and gives rise to the nonstaggered architecture.
History
DepositionJul 12, 2016-
Header (metadata) releaseJul 27, 2016-
Map releaseJul 27, 2016-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5jyg
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5jyg
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8180.png

Downloads & links

-
Map

FileDownload / File: emd_8180.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 320 pix.
= 403.2 Å		1.26 Å/pix.
x 320 pix.
= 403.2 Å		1.26 Å/pix.
x 320 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-5.3581657 - 11.790862000000001
Average (Standard dev.)0.000000000091066 (±0.6944725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 403.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z403.200403.200403.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-5.35811.7910.000

-
Supplemental data

-
Sample components

-
Entire : Magnetosome-associated MamK filament

EntireName: Magnetosome-associated MamK filament
Components
  • Organelle or cellular component: Magnetosome-associated MamK filament
    • Protein or peptide: Actin-like ATPase
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: Magnetosome-associated MamK filament

SupramoleculeName: Magnetosome-associated MamK filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: ADP-bound MamK
Source (natural)Organism: Magnetospirillum magneticum AMB-1 (bacteria)

-
Macromolecule #1: Actin-like ATPase

MacromoleculeName: Actin-like ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) (bacteria)
Strain: AMB-1 / ATCC 700264
Molecular weightTheoretical: 37.65618 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSEGEGQAKN RLFLGIDLGT SHTAVMSSRG KKFLLKSVVG YPKDVIGLKL LGRPYVVGDE AFEMRSYLDI RYPLQDGVLS EISDRDIEV ARHLLTHVVK SAEPGPNDEI CAVIGVPARA SAANKALLLK MAQEVVHTAL VVSEPFMVGY GLDKLINTII V DIGAGTTD ...String:
MSEGEGQAKN RLFLGIDLGT SHTAVMSSRG KKFLLKSVVG YPKDVIGLKL LGRPYVVGDE AFEMRSYLDI RYPLQDGVLS EISDRDIEV ARHLLTHVVK SAEPGPNDEI CAVIGVPARA SAANKALLLK MAQEVVHTAL VVSEPFMVGY GLDKLINTII V DIGAGTTD ICALKGTVPG PEDQVTLTKA GNYVDERLQN AILERHPELQ MNVNVACAVK EQFSFVGTPT EVASFEFRAA GK PVRADVT EPVKIACEAL MPDIIESIET LLRSFQPEYQ ATVLQNIVFA GGGSRIRGLA AYVKEKLRPF GDANVTCVKD PTF DGCRGA LRLAEELPPQ YWRQLGDVSG S

UniProtKB: Actin-like protein MamK

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 14 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 14 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 53.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 24 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8129
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE

-
Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-5jyg:
Cryo-EM structure of the MamK filament at 6.5 A

+
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