[English] 日本語
Yorodumi
- EMDB-51470: Cryo-EM structure of essential Mycoplasma pneumoniae lipoprotein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51470
TitleCryo-EM structure of essential Mycoplasma pneumoniae lipoprotein Mpn444 homotrimer
Map data
Sample
  • Complex: Essential Mycoplasma pneumoniae lipoprotein Mpn444 homotrimer
    • Protein or peptide: Uncharacterized lipoprotein MG309 homolog
KeywordsLipoprotein Surface Protein Mycoplasma pneumoniae / UNKNOWN FUNCTION
Function / homologyProtein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / Uncharacterized lipoprotein MG309 homolog
Function and homology information
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsManger S / Keles I
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: To Be Published
Title: Structural characterization of an essential lipoprotein of Mycoplasma pneumoniae
Authors: Keles I / Manger S / Frangakis AS
History
DepositionSep 3, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51470.png

Downloads & links

-
Map

FileDownload / File: emd_51470.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 480 pix.
= 441.6 Å		0.92 Å/pix.
x 480 pix.
= 441.6 Å		0.92 Å/pix.
x 480 pix.
= 441.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0495
Minimum - Maximum-0.21122153 - 0.28153595
Average (Standard dev.)-0.000072612136 (±0.008459684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 441.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51470_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51470_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51470_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Essential Mycoplasma pneumoniae lipoprotein Mpn444 homotrimer

EntireName: Essential Mycoplasma pneumoniae lipoprotein Mpn444 homotrimer
Components
  • Complex: Essential Mycoplasma pneumoniae lipoprotein Mpn444 homotrimer
    • Protein or peptide: Uncharacterized lipoprotein MG309 homolog

-
Supramolecule #1: Essential Mycoplasma pneumoniae lipoprotein Mpn444 homotrimer

SupramoleculeName: Essential Mycoplasma pneumoniae lipoprotein Mpn444 homotrimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

-
Macromolecule #1: Uncharacterized lipoprotein MG309 homolog

MacromoleculeName: Uncharacterized lipoprotein MG309 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 144.800641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MCAQPTASTV EGLFKPSSAF ADRTDFSLSS ILQKSLINRE SFNQYLAMRL APVLRTFYED NYDTDIKERL NGFTADTDNA FVSQEQNLR NQFRENYLVH LQTDIFDNTG GNQAAWKLRD VNNKIIDDFI SRIFAKNFVE YVQDGVGPLT KPTKSLIENT S NFKNIKLQ ...String:
MCAQPTASTV EGLFKPSSAF ADRTDFSLSS ILQKSLINRE SFNQYLAMRL APVLRTFYED NYDTDIKERL NGFTADTDNA FVSQEQNLR NQFRENYLVH LQTDIFDNTG GNQAAWKLRD VNNKIIDDFI SRIFAKNFVE YVQDGVGPLT KPTKSLIENT S NFKNIKLQ PKFVNKNAKL KINNDAVYAA IQDKLLDQFI TNENPNLVSR VVFTNETPVD GFDNYFNTKV IQSPTPSYQF QV FNKYNQQ SGGTKGANGF NLLASNLKSY KNDQSKGIDI PNKFSSDSGG KLLLKASDMF DTFDPSFSAA FIQGYLALQK KSK GADSKE VDSLIKDKSI IENFFVDNNT QAAAAARAAS SSSEGTIQLK TASDGGGTTQ STVHKTDLVK IFGDKDVFAG EYKQ QIGNT NANQTGGGGS GGGGGTSTGS STGSSTETTT GNSSKAVVDL IEVKKDSSSQ PDYILSRGKD GIHLMAVDGG SHYLT ESGR DVAKQKKFLL FRALQTKYGL VDTDTTYDFK LFDEVKKYFD TNRILFLFEA LLDLSSDTNN KDNFLSYPQF KKFADS IKS IEKDLKELVQ AHYKQAVFNE TAVAENKVTL KLAERNQPFI DNERNNQIEQ NGLAAKLPYE QDAKTGHYND LGNYYKD II DNVDKKGTST VKTTSSNTGQ TKNFSEEVVS KLKDNKKKVE EAAKKHVEAL KVFTIPSPLY SQVILVQTKL SFTPESTS L GLNLALNNYL TSTELQNSIK LSYFQEDEAF KKIIDITNLT FSQQSGGTGG TNGNNNLTAD NWKIFKETYL LDLFESQAQ KSIFGHVGSS DKNSSTKTGI EGVLDTLYSS LNLEERLDSD DVIDYLSYLY TAHWLLKDNL KNYKQSLQSK LSRTSNAFLV WSVDSEKNK NDSQSTLSST ASSTSNTGLI QLRSVVSLAQ NQAAGQGGDN NSDITQTEVK NPNFVFGSSV YDWTNSKTPE V NRAADDTS SFFYTKSSSS STGAAQSSAT VLRSLNQASG MTTKTAKNRY GFRGIVTSST SGSLPEAVSR RLFKQFVNQT EK GVKVGGQ MLITTAKSGK ATLVLKQQAD DAESTTNNAY KGALFSFGSM DNLKNIINGI QTQTEFDALY NHLTSDLNID VTG VDKNKT LTEQKTSLTS FVDSNFKQST QSAQRGDTSA RSARSATVQI KKTQEDNQNT NYKDVFSRFD GYIGDNKVEE KNYT SYQFL SDGGKYHATF VKQVNLDDVE KIGTDSLKQE DSSKDKRLNL SLEEFLAAIA LEALDPNNQT QAINALISGN KKGLV KVGD FRIFSSISAQ WVRRFAAALE HHHHHH

UniProtKB: Uncharacterized lipoprotein MG309 homolog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
Details: 20 mM Tris-HCl 200 mM NaCl 0-0.01% LMNG or 1 mM CHAPSO
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 7811 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3376184
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 626110
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.3)

+
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