[English] 日本語
Yorodumi
- EMDB-3122: A Spiral Scaffold Underlies Cytoadherent Knobs in Plasmodium falc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3122
TitleA Spiral Scaffold Underlies Cytoadherent Knobs in Plasmodium falciparum-Infected Erythrocytes
Map dataCryo-tomogram of Plasmodium falciparum schizont skeleton labelled with anti-KAHRP antibody
Sample
  • Sample: Detergent-insoluble skeleton of Plasmodium falciparum schizont, labelled with anti-KAHRP antibody mAb 18.2 and gold-conjugated secondary antibody
  • Organelle or cellular component: cytoskeleton
Keywordsmalaria / Plasmodium / knobs / cytoadherence / KAHRP / erythrocyte / skeleton / schizont / blood
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodelectron tomography / cryo EM
AuthorsWatermeyer JM / Hale VL / Hackett F / Clare DK / Cutts EE / Vakonakis I / Fleck RA / Blackman MJ / Saibil HR
CitationJournal: Blood / Year: 2016
Title: A spiral scaffold underlies cytoadherent knobs in Plasmodium falciparum-infected erythrocytes.
Authors: Jean M Watermeyer / Victoria L Hale / Fiona Hackett / Daniel K Clare / Erin E Cutts / Ioannis Vakonakis / Roland A Fleck / Michael J Blackman / Helen R Saibil /
Abstract: Much of the virulence of Plasmodium falciparum malaria is caused by cytoadherence of infected erythrocytes, which promotes parasite survival by preventing clearance in the spleen. Adherence is ...Much of the virulence of Plasmodium falciparum malaria is caused by cytoadherence of infected erythrocytes, which promotes parasite survival by preventing clearance in the spleen. Adherence is mediated by membrane protrusions known as knobs, whose formation depends on the parasite-derived, knob-associated histidine-rich protein (KAHRP). Knobs are required for cytoadherence under flow conditions, and they contain both KAHRP and the parasite-derived erythrocyte membrane protein PfEMP1. Using electron tomography, we have examined the 3-dimensional structure of knobs in detergent-insoluble skeletons of P falciparum 3D7 schizonts. We describe a highly organized knob skeleton composed of a spiral structure coated by an electron-dense layer underlying the knob membrane. This knob skeleton is connected by multiple links to the erythrocyte cytoskeleton. We used immuno-electron microscopy (EM) to locate KAHRP in these structures. The arrangement of membrane proteins in the knobs, visualized by high-resolution freeze-fracture scanning EM, is distinct from that in the surrounding erythrocyte membrane, with a structure at the apex that likely represents the adhesion site. Thus, erythrocyte knobs in P falciparum infection contain a highly organized skeleton structure underlying a specialized region of membrane. We propose that the spiral and dense coat organize the cytoadherence structures in the knob, and anchor them into the erythrocyte cytoskeleton. The high density of knobs and their extensive mechanical linkage suggest an explanation for the rigidification of the cytoskeleton in infected cells, and for the transmission to the cytoskeleton of shear forces experienced by adhering cells.
History
DepositionAug 11, 2015-
Header (metadata) releaseAug 26, 2015-
Map releaseDec 23, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3122.tif

Downloads & links

-
Map

FileDownload / File: emd_3122.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationCryo-tomogram of Plasmodium falciparum schizont skeleton labelled with anti-KAHRP antibody
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.78 Å/pix.
x 285 pix.
= 3072.3 Å		10.78 Å/pix.
x 1920 pix.
= 20697.6 Å		10.78 Å/pix.
x 1856 pix.
= 20007.68 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.78 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum0.0 - 32510.0
Average (Standard dev.)16948.41796875 (±1218.615600589999985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00133
Dimensions19201856285
Spacing19201856285
CellA: 20007.68 Å / B: 20697.6 Å / C: 3072.2998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z10.7810.7810.78
M x/y/z18561920285
origin x/y/z0.0000.0000.000
length x/y/z20007.68020697.6003072.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00133
NC/NR/NS18561920285
D min/max/mean0.00032510.00016948.418

-
Supplemental data

-
Sample components

-
Entire : Detergent-insoluble skeleton of Plasmodium falciparum schizont, l...

EntireName: Detergent-insoluble skeleton of Plasmodium falciparum schizont, labelled with anti-KAHRP antibody mAb 18.2 and gold-conjugated secondary antibody
Components
  • Sample: Detergent-insoluble skeleton of Plasmodium falciparum schizont, labelled with anti-KAHRP antibody mAb 18.2 and gold-conjugated secondary antibody
  • Organelle or cellular component: cytoskeleton

-
Supramolecule #1000: Detergent-insoluble skeleton of Plasmodium falciparum schizont, l...

SupramoleculeName: Detergent-insoluble skeleton of Plasmodium falciparum schizont, labelled with anti-KAHRP antibody mAb 18.2 and gold-conjugated secondary antibody
type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: cytoskeleton

SupramoleculeName: cytoskeleton / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
synonym: malaria parasite / Location in cell: erythrocyte cytoskeleton

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
GridDetails: 300 mesh gold Quantifoil grid R3.5/1
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: Gatan Quantum
Detailscounting mode
DateJul 6, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Average electron dose: 114 e/Å2
Details: Images were the average of 20 subframes recorded by the direct electron detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 7.0 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 64 ° / Tilt series - Axis1 - Angle increment: 2 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 63
CTF correctionDetails: each image

+
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