[English] 日本語
Yorodumi
- EMDB-7017: Segment from bank vole prion protein 168-176 QYNNQNNFV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7017
TitleSegment from bank vole prion protein 168-176 QYNNQNNFV
Map dataprotein segment
Sample
  • Complex: bank vole prion 168-176
    • Protein or peptide: Major prion protein
  • Ligand: water
Keywordspolar clasp / amyloid fibril / prion / PROTEIN FIBRIL
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / plasma membrane
Similarity search - Function
Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
Biological speciesMyodes glareolus (Bank vole)
Methodelectron crystallography / cryo EM
AuthorsGlynn C / Rodriguez JA
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp.
Authors: Marcus Gallagher-Jones / Calina Glynn / David R Boyer / Michael W Martynowycz / Evelyn Hernandez / Jennifer Miao / Chih-Te Zee / Irina V Novikova / Lukasz Goldschmidt / Heather T McFarlane / ...Authors: Marcus Gallagher-Jones / Calina Glynn / David R Boyer / Michael W Martynowycz / Evelyn Hernandez / Jennifer Miao / Chih-Te Zee / Irina V Novikova / Lukasz Goldschmidt / Heather T McFarlane / Gustavo F Helguera / James E Evans / Michael R Sawaya / Duilio Cascio / David S Eisenberg / Tamir Gonen / Jose A Rodriguez /
Abstract: The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution ...The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.
History
DepositionSep 7, 2017-
Header (metadata) releaseNov 1, 2017-
Map releaseJan 17, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.44
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.44
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6axz
  • Surface level: 0.44
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7017.png

Downloads & links

-
Map

FileDownload / File: emd_7017.map.gz / Format: CCP4 / Size: 484.4 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprotein segment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
0.24 Å/pix.
x 44 pix.
= 10.34 Å		0.22 Å/pix.
x 22 pix.
= 4.94 Å		0.24 Å/pix.
x 128 pix.
= 31.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.22455 Å / Y: 0.235 Å / Z: 0.24336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44 / Movie #1: 0.44
Minimum - Maximum-0.719746 - 3.6190872
Average (Standard dev.)-0.000000000425498 (±0.3238952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions2212844
Spacing2244128
CellA: 4.94 Å / B: 10.34 Å / C: 31.15 Å
α: 94.205 ° / β: 92.375 ° / γ: 102.204 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.224545454545450.2350.243359375
M x/y/z2244128
origin x/y/z0.0000.0000.000
length x/y/z4.94010.34031.150
α/β/γ94.20592.375102.204
start NX/NY/NZ000
NX/NY/NZ2244128
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS1282244
D min/max/mean-0.7203.619-0.000

-
Supplemental data

-
Sample components

-
Entire : bank vole prion 168-176

EntireName: bank vole prion 168-176
Components
  • Complex: bank vole prion 168-176
    • Protein or peptide: Major prion protein
  • Ligand: water

-
Supramolecule #1: bank vole prion 168-176

SupramoleculeName: bank vole prion 168-176 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Myodes glareolus (Bank vole)
Molecular weightTheoretical: 4.6 KDa

-
Macromolecule #1: Major prion protein

MacromoleculeName: Major prion protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Myodes glareolus (Bank vole)
Molecular weightTheoretical: 1.140162 KDa
SequenceString:
QYNNQNNFV

UniProtKB: Major prion protein

-
Macromolecule #2: water

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

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.025 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 950 mm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES
Crystallography statisticsNumber intensities measured: 43252 / Number structure factors: 7474 / Fourier space coverage: 97.1 / R sym: 23.2 / R merge: 23.2 / Overall phase error: 0.01 / Overall phase residual: 0.01 / Phase error rejection criteria: 0 / High resolution: 0.75 Å / Shell - Shell ID: 1 / Shell - High resolution: 0.75 Å / Shell - Low resolution: 0.77 Å / Shell - Number structure factors: 532 / Shell - Phase residual: 0.01 / Shell - Fourier space coverage: 96.2 / Shell - Multiplicity: 4.4

-
Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 6.068 / Target criteria: maximum likelihood
Output model

PDB-6axz:
Segment from bank vole prion protein 168-176 QYNNQNNFV

+
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