[English] 日本語
Yorodumi
- EMDB-51409: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51409
TitleMycoplasma pneumoniae protein P116 ectodomain in the full conformation
Map data
Sample
  • Complex: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation
    • Protein or peptide: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation
KeywordsMycoplasma pneumoniae Lipid Transfer Lipid Transport / LIPID BINDING PROTEIN
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsManger S
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Essential protein P116 extracts cholesterol and other indispensable lipids for Mycoplasmas.
Authors: Lasse Sprankel / David Vizarraga / Jesús Martín / Sina Manger / Jakob Meier-Credo / Marina Marcos / Josep Julve / Noemi Rotllan / Margot P Scheffer / Joan Carles Escolà-Gil / Julian D ...Authors: Lasse Sprankel / David Vizarraga / Jesús Martín / Sina Manger / Jakob Meier-Credo / Marina Marcos / Josep Julve / Noemi Rotllan / Margot P Scheffer / Joan Carles Escolà-Gil / Julian D Langer / Jaume Piñol / Ignacio Fita / Achilleas S Frangakis /
Abstract: Mycoplasma pneumoniae, responsible for approximately 30% of community-acquired human pneumonia, needs to extract lipids from the host environment for survival and proliferation. Here, we report a ...Mycoplasma pneumoniae, responsible for approximately 30% of community-acquired human pneumonia, needs to extract lipids from the host environment for survival and proliferation. Here, we report a comprehensive structural and functional analysis of the previously uncharacterized protein P116 (MPN_213). Single-particle cryo-electron microscopy of P116 reveals a homodimer presenting a previously unseen fold, forming a huge hydrophobic cavity, which is fully accessible to solvent. Lipidomics analysis shows that P116 specifically extracts lipids such as phosphatidylcholine, sphingomyelin and cholesterol. Structures of different conformational states reveal the mechanism by which lipids are extracted. This finding immediately suggests a way to control Mycoplasma infection by interfering with lipid uptake.
History
DepositionAug 23, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51409.png

Downloads & links

-
Map

FileDownload / File: emd_51409.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 537.6 Å		1.05 Å/pix.
x 512 pix.
= 537.6 Å		1.05 Å/pix.
x 512 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.141
Minimum - Maximum-1.3696263 - 2.4689045
Average (Standard dev.)-0.00016761584 (±0.013920468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51409_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51409_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51409_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mycoplasma pneumoniae protein P116 ectodomain in the full conformation

EntireName: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation
Components
  • Complex: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation
    • Protein or peptide: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation

-
Supramolecule #1: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation

SupramoleculeName: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)

-
Macromolecule #1: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation

MacromoleculeName: Mycoplasma pneumoniae protein P116 ectodomain in the full conformation
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLSAIISLS VAGTVGTTA V VVPTTITL VN KTHQVEH ESE QSDFQD IRFG LNSVK LPKAQ PAAA TRITVE NGT DKLVNYK SS PQQLFLAK N ALKDKLQGE FDKFLSDAKA FPALTADLQ E WVDQQLFN PN QSFFDLS APR SNFTLS SDKK ASLDF ...String:
MKLSAIISLS VAGTVGTTA V VVPTTITL VN KTHQVEH ESE QSDFQD IRFG LNSVK LPKAQ PAAA TRITVE NGT DKLVNYK SS PQQLFLAK N ALKDKLQGE FDKFLSDAKA FPALTADLQ E WVDQQLFN PN QSFFDLS APR SNFTLS SDKK ASLDF IFRFT NFTE SVQLLK LPE GVSVVVD SK QSFDYYVN A SAQKLLVLP LSLPDYTLGL NYMFDHITL N GKVVNKFS FN PFKTNLN LAF SNVYNG VDVF EAQKN LVGKG KYLN THVKAE DVK KDVNANI KN QFDIAKII A ELMGKALKE FGNQQEGQPL SFLKVMDKV K EDFEKLFN LV RPGLGKF VKD LIQSSS QAEN KITVY KLIFD NKKT ILNLLK ELS IPELNSS LG LVDVLFDG I TDSDGLYER LQSFKDLIVP AVKTNEKTA A LSPLIEEL LT QKDTYVF DLI QKHKGI LTNL LKNFL ADFQK STPF MADQVA IFT ELFDNEG AF DLFGEADF V DKIAELFLT KRTVKNGEKI ETKDSLLVT S LKSLLGEK VA ALGDLLD SYI FKNELL NRSV EVAKA EAKDT KGAT DYKKEQ AKA LKKLFKH IG ENTLSKTN L DKITLKEVK NTENVELEET ETTLKVKKL D VEYKVELG NF EIKNGLI KAM LEFLPD TKDL ETTLD KLLFK GESY KAMKDK YIK EGFPGYG WA KGVVPGAF E SIENTFKSA IDKTKSIRDL FGDMLFGND L SSVKETDS FI TLGGSFD IKY GGENLN VLPA YYSLI NSEIG YQII GVDTTI DAT KVKVELK NK EYKGKSPA I NGQVKLSQS FFNVWTNMFD SITKQIFQK K YEFKDNIQ VF ARNEDNT SRL ELDISD PEQR VIPFA FVDGF GIQL KAVDKN ITK EAGNTEP KS PVIQLYEA L NKEKDQKQQ SKQSPKQLDT KTQLGYLLK L GDNWSKDD YK SLIDDTI INN NYLEAS FNSK ITVDR LGIPI DLWL FKIWPK FNL EIPMQGS LQ LYSSSVIF P YGIYDTSVQ DAAKIVKRLN FTDMGFKLN D PKPNFWFV GF

-
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
GridModel: C-flat-1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
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 K2 SUMMIT (4k x 4k) / 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: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3836309
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 834674
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - 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