[English] 日本語
Yorodumi
- EMDB-2892: Cryo-Molecular electron tomography of complex of human non-immune... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2892
TitleCryo-Molecular electron tomography of complex of human non-immune soluble pentameric IgM and PfEMP1-IT4Var60 in 1:1 ratio
Map dataReconstruction of IgM-PfEMP1 complex in 1:1 ratio str2
Sample
  • Sample: Human pentameric IgM-PfEMP1 complex in 1:1 ratio str2
  • Protein or peptide: Immunoglobulin M
  • Protein or peptide: PfEMP1 complex
KeywordsMalaria / Rosetting / IgM / PfEMP1 / complex
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodelectron tomography / cryo EM / Resolution: 20.0 Å
AuthorsAkhouri RR / Goel S / Furusho H / Skoglund U / Wahlgren M
CitationJournal: Cell Rep / Year: 2016
Title: Architecture of Human IgM in Complex with P. falciparum Erythrocyte Membrane Protein 1.
Authors: Reetesh Raj Akhouri / Suchi Goel / Hirotoshi Furusho / Ulf Skoglund / Mats Wahlgren /
Abstract: Plasmodium falciparum virulence is associated with sequestration of infected erythrocytes. Microvascular binding mediated by PfEMP1 in complex with non-immune immunoglobulin M (IgM) is common among ...Plasmodium falciparum virulence is associated with sequestration of infected erythrocytes. Microvascular binding mediated by PfEMP1 in complex with non-immune immunoglobulin M (IgM) is common among parasites that cause both severe childhood malaria and pregnancy-associated malaria. Here, we present cryo-molecular electron tomography structures of human IgM, PfEMP1 and their complex. Three-dimensional reconstructions of IgM reveal that it has a dome-like core, randomly oriented Fab2s units, and the overall shape of a turtle. PfEMP1 is a C- shaped molecule with a flexible N terminus followed by an arc-shaped backbone and a bulky C terminus that interacts with IgM. Our data demonstrate that the PfEMP1 binding pockets on IgM overlap with those of C1q, and the bulkiness of PfEMP1 limits the capacity of IgM to interact with PfEMP1. We suggest that P. falciparum exploits IgM to cluster PfEMP1 into an organized matrix to augment its affinity to host cell receptors.
History
DepositionFeb 8, 2015-
Header (metadata) releaseFeb 25, 2015-
Map releaseJan 13, 2016-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0098
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0098
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2892.tif

Downloads & links

-
Map

FileDownload / File: emd_2892.map.gz / Format: CCP4 / Size: 886.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of IgM-PfEMP1 complex in 1:1 ratio str2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.53 Å/pix.
x 77 pix.
= 349.118 Å		4.53 Å/pix.
x 45 pix.
= 204.03 Å		4.53 Å/pix.
x 67 pix.
= 303.778 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.534 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0098 / Movie #1: 0.0098
Minimum - Maximum0.00007028 - 0.02325541
Average (Standard dev.)0.00450668 (±0.00371983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions456777
Spacing456777
CellA: 303.77798 Å / B: 204.03 Å / C: 349.11798 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.5344.5344.534
M x/y/z674577
origin x/y/z0.0000.0000.000
length x/y/z303.778204.030349.118
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS674577
D min/max/mean0.0000.0230.005

-
Supplemental data

-
Sample components

-
Entire : Human pentameric IgM-PfEMP1 complex in 1:1 ratio str2

EntireName: Human pentameric IgM-PfEMP1 complex in 1:1 ratio str2
Components
  • Sample: Human pentameric IgM-PfEMP1 complex in 1:1 ratio str2
  • Protein or peptide: Immunoglobulin M
  • Protein or peptide: PfEMP1 complex

-
Supramolecule #1000: Human pentameric IgM-PfEMP1 complex in 1:1 ratio str2

SupramoleculeName: Human pentameric IgM-PfEMP1 complex in 1:1 ratio str2 / type: sample / ID: 1000
Details: the sample was polydisperse using Dynamic Light Scattering.
Oligomeric state: one PfEMP1 bound to one IgM / Number unique components: 2
Molecular weightExperimental: 1.35 MDa / Theoretical: 1.3 MDa

-
Macromolecule #1: Immunoglobulin M

MacromoleculeName: Immunoglobulin M / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
synonym: malaria parasite / Location in cell: infected erythrocyte membrane
Molecular weightExperimental: 1.35 MDa / Theoretical: 1.3 MDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly) / Recombinant cell: S2 cells / Recombinant plasmid: pMTBipV5HisA

-
Macromolecule #2: PfEMP1 complex

MacromoleculeName: PfEMP1 complex / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
synonym: malaria parasite / Location in cell: infected erythrocyte membrane
Molecular weightExperimental: 1.35 MDa / Theoretical: 1.3 MDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly) / Recombinant cell: S2 cells / Recombinant plasmid: pMTBipV5HisA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5 / Details: 20mM Tris, 200mM NaCl
GridDetails: C-Flat (Copper grid with thin Carbon support)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 78 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 4 seconds before plunging

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78 K / Max: 100 K
Specialist opticsEnergy filter - Name: FEI
DateJun 13, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 281 / Average electron dose: 40 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0015 µm / Nominal defocus min: 0.0007 µm / Nominal magnification: 37000
Sample stageSpecimen holder: LN2 cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 ° / Tilt series - Axis1 - Angle increment: 0.5 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsCTF correction on each tilt
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Software - Name: COMET / Number images used: 281
CTF correctionDetails: each frame

+
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