[English] 日本語
Yorodumi
- EMDB-51308: Cryo-EM Structure of Pentameric Outer Membrane Protein A from Bde... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51308
TitleCryo-EM Structure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus
Map dataOverall Map
Sample
  • Complex: Pentameric Outer Membrane protein A, PopA
    • Protein or peptide: Major outer membrane protein
  • Ligand: water
KeywordsOuter membrane protein / porin / beta-barrel / LIPID BINDING PROTEIN
Function / homologyMajor outer membrane protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsParr RJ / Ratkeviciute G / Lovering AL
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust209437/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M01116X/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_17136 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: A porin-like protein used by bacterial predator defines a wider lipid-trapping superfamily
Authors: Parr RJ / Lovering AL
History
DepositionAug 8, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51308.png

Downloads & links

-
Map

FileDownload / File: emd_51308.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 250.5 Å		0.84 Å/pix.
x 300 pix.
= 250.5 Å		0.84 Å/pix.
x 300 pix.
= 250.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-1.0763147 - 1.5214568
Average (Standard dev.)0.0011521117 (±0.041213065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 250.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51308_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51308_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51308_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pentameric Outer Membrane protein A, PopA

EntireName: Pentameric Outer Membrane protein A, PopA
Components
  • Complex: Pentameric Outer Membrane protein A, PopA
    • Protein or peptide: Major outer membrane protein
  • Ligand: water

-
Supramolecule #1: Pentameric Outer Membrane protein A, PopA

SupramoleculeName: Pentameric Outer Membrane protein A, PopA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bdellovibrio bacteriovorus HD100 (bacteria)

-
Macromolecule #1: Major outer membrane protein

MacromoleculeName: Major outer membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bdellovibrio bacteriovorus HD100 (bacteria)
Molecular weightTheoretical: 37.092637 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SKARVEALAN SRHVLDFQTA FDRPYQFMAL SEQATIEWGN TGDANPHAEG GFVKRHGDDS AFGAYFGRRS ADFSEAVQTV RDASSHHHH HHGSSNPAFA DLMFEQNGLN LFYASKMGEW TWGVTAKYSN GKNEDPTVGT KATSAGVAVA ASNGTWDFEL V QGFTGKSE ...String:
SKARVEALAN SRHVLDFQTA FDRPYQFMAL SEQATIEWGN TGDANPHAEG GFVKRHGDDS AFGAYFGRRS ADFSEAVQTV RDASSHHHH HHGSSNPAFA DLMFEQNGLN LFYASKMGEW TWGVTAKYSN GKNEDPTVGT KATSAGVAVA ASNGTWDFEL V QGFTGKSE LDNGTVTAEV ESKGLTNVTV GYHMSPEMEV YGNVKMSKVE ADLNGTPIEV ETTSYKVGMV NTLAKSEEGN FF YGVEVAS TKVKDDSESL LLPVYMGVEH NAASWLVLRA SVAQNVILNE TKDDATGNKT DEDSTRMAAG AGIKFGKSVI DAS FAGSTT GVINANNLFS QVAYTYTF

UniProtKB: Major outer membrane protein

-
Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 33 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSodium ChlorideNaCl
0.03 (w/v) %n-dodecyl-beta-D-maltoside (DDM)C24H46O11
GridModel: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 992500
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Software - details: Punjani et al., 2017 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-inition
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 365835
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: Crystallographic stucture
RefinementProtocol: OTHER
Output model

PDB-9gf0:
Cryo-EM Structure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus

+
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