[English] 日本語
- EMDB-6876: Cryo-EM structure of Methanoccus maripaludis archaellum -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 6876
TitleCryo-EM structure of Methanoccus maripaludis archaellum
Map dataMethanococcus maripaludis archaellum cryo-EM reconstruction
SampleM.maripaludis archaellin FlaB1 filament:
Function / homologyFlagellin, archaea / Flagellin/pilin, N-terminal / Archaebacterial flagellin / archaeal-type flagellum / structural molecule activity / integral component of membrane / Flagellin
Function and homology information
SourceMethanococcus maripaludis S2 (archaea) / Methanococcus maripaludis (strain S2 / LL) (archaea)
Methodhelical reconstruction / cryo EM / 4 Å resolution
AuthorsMeshcheryakov VA / Shibata S / Schreiber MT / Villar-Briones A / Jarrell KF / Aizawa S / Wolf M
CitationJournal: To Be Published
Title: Cryo-EM structure of Methanoccus maripaludis archaellum
Authors: Meshcheryakov VA / Shibata S / Schreiber MT / Villar-Briones A / Jarrell KF / Aizawa S / Wolf M
Validation ReportPDB-ID: 5z1l

SummaryFull reportAbout validation report
DateDeposition: Dec 26, 2017 / Header (metadata) release: Feb 13, 2019 / Map release: Feb 13, 2019 / Last update: Feb 13, 2019

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5z1l
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_6876.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
1.41 Å/pix.
= 180.48 Å
128 pix
1.41 Å/pix.
= 180.48 Å
128 pix
1.41 Å/pix.
= 180.48 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.41 Å
Contour Level:3.0 (by author), 3 (movie #1):
Minimum - Maximum-11.208774 - 14.403278999999999
Average (Standard dev.)-0.000000002624336 (0.9999997)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 180.48 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.411.411.41
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z180.480180.480180.480
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-64-64-64
D min/max/mean-11.20914.403-0.000

Supplemental data

Sample components

Entire M.maripaludis archaellin FlaB1 filament

EntireName: M.maripaludis archaellin FlaB1 filament / Number of components: 2

Component #1: protein, M.maripaludis archaellin FlaB1 filament

ProteinName: M.maripaludis archaellin FlaB1 filament / Recombinant expression: No
SourceSpecies: Methanococcus maripaludis S2 (archaea)

Component #2: protein, Flagellin

ProteinName: Flagellin / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 21.639359 kDa
SourceSpecies: Methanococcus maripaludis (strain S2 / LL) (archaea)
Strain: S2 / LL

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: .8 mg/ml / pH: 7
Support filmGatan Solarus
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 289 K / Humidity: 100 % / Details: 3 second blot, 3.5uL.

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: nanoprobe, parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 96 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal), 47619.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1500.0 - -2500.0 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 77.0 - 100.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 2000 / Sampling size: 5 microns

Image processing

ProcessingMethod: helical reconstruction
Details: frame alignment and integration with motioncor2 incl. dose weighting and 2x Fourier cropping
3D reconstructionAlgorithm: FOURIER SPACE / Software: SPRING / CTF correction: deconvolution in SPRING / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: segmentrefine3d

Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Output model

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more


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.

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