[English] 日本語
Yorodumi
- PDB-7rvd: Segment from the mouse/cow prion protein 168-176 QYSNQNNFV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rvd
TitleSegment from the mouse/cow prion protein 168-176 QYSNQNNFV
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid / prion / fibril / mouse / cow
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / positive regulation of glutamate receptor signaling pathway / lamin binding / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / type 5 metabotropic glutamate receptor binding ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / positive regulation of glutamate receptor signaling pathway / lamin binding / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / cupric ion binding / nucleobase-containing compound metabolic process / activation of protein kinase activity / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / response to amyloid-beta / cuprous ion binding / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / intracellular copper ion homeostasis / regulation of peptidyl-tyrosine phosphorylation / negative regulation of protein phosphorylation / response to cadmium ion / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / molecular function activator activity / positive regulation of protein localization to plasma membrane / negative regulation of DNA-binding transcription factor activity / molecular condensate scaffold activity / terminal bouton / protein destabilization / protein homooligomerization / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / regulation of protein localization / amyloid-beta binding / protein-folding chaperone binding / protease binding / microtubule binding / nuclear membrane / molecular adaptor activity / transmembrane transporter binding / response to oxidative stress / learning or memory / postsynaptic density / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
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 speciesMus musculus (house mouse)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / AB INITIO PHASING / Resolution: 1.003 Å
AuthorsGlynn, C. / Rodriguez, J.A. / Hernandez, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128867 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F31AI143368 United States
CitationJournal: To be published
Title: Structural and Biophysical Consequences of Sequence Variation in the B2a2 Loop of Mammalian Prions
Authors: Glynn, C. / Rodriguez, J.A. / Hernandez, E.
History
DepositionAug 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)1,1131
Polymers1,1131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1380 Å2
Unit cell
Length a, b, c (Å)4.870, 10.170, 31.290
Angle α, β, γ (deg.)94.650, 90.730, 101.150
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide Major prion protein / PrP / PrP27-30 / PrP33-35C


Mass: 1113.137 Da / Num. of mol.: 1 / Fragment: UNP residues 167-175 / Source method: obtained synthetically / Details: also Bos taurus / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P04925

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 1
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

-
Sample preparation

ComponentName: Major prion protein / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.5 M zinc acetate, 15% ethanol, 0.2 M MES, pH 6

-
Data collection

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1
EM diffractionCamera length: 1 mm
DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: OTHER / Wavelength: 0.0251 Å
DetectorType: TVIPS TEMCAM-F416 / Detector: CMOS / Date: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1→10.391 Å / Num. obs: 2977 / % possible obs: 93.9 % / Redundancy: 2.996 % / Biso Wilson estimate: 4.54 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.197 / Χ2: 0.952 / Net I/σ(I): 3.99 / Num. measured all: 8918 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1-1.032.4330.5141.335232272150.7420.6594.7
1.03-1.052.540.4781.514802071890.8060.59891.3
1.05-1.082.5120.3172.155402322150.9060.39392.7
1.08-1.122.7680.2852.686202352240.9050.34795.3
1.12-1.153.0250.3342.985992101980.860.39994.3
1.15-1.23.1330.2963.096582222100.9350.35594.6
1.2-1.242.7980.2712.935121911830.9280.32995.8
1.24-1.293.0060.2743.364871681620.9390.32596.4
1.29-1.352.9180.2373.54641661590.9390.28495.8
1.35-1.413.1170.2463.835331811710.9220.29494.5
1.41-1.493.40.2224.755441711600.9450.26193.6
1.49-1.583.4910.2015.165691701630.9690.23395.9
1.58-1.693.4440.176.124651471350.9490.19891.8
1.69-1.832.970.1635.542971081000.9640.19992.6
1.83-23.1880.1536.434081371280.9870.18293.4
2-2.243.2290.1217.33391121050.9860.14593.8
2.24-2.583.7140.1268.26364108980.9720.14690.7
2.58-3.163.030.097.7120374670.9940.10690.5
3.16-4.473.2770.1298.8521370650.9880.15192.9
4.47-10.3913.3330.1717.8110034300.9750.19488.2

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXDphasing
EM 3D crystal entity∠α: 94.65 ° / ∠β: 90.73 ° / ∠γ: 101.15 ° / A: 4.87 Å / B: 10.17 Å / C: 31.29 Å / Space group name: P1 / Space group num: 1
3D reconstructionResolution: 1.003 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.003→10.391 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 265 9.03 %
Rwork0.2011 2670 -
obs0.2056 2935 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 40.87 Å2 / Biso mean: 8.4907 Å2 / Biso min: 1.19 Å2
Refinement stepCycle: final / Resolution: 1.003→10.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms79 0 0 0 79
Num. residues----9
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00880
ELECTRON CRYSTALLOGRAPHYf_angle_d0.92108
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.09610
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.00516
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d15.24928
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.0035-1.26390.25661290.1994130091
1.2639-100.24711360.2019137097

+
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