[English] 日本語
Yorodumi
- PDB-4j8r: Structure of an octapeptide repeat of the prion protein bound to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j8r
TitleStructure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody fragment
Components
  • Heavy chain of POM2 Fab
  • Light chain of POM2 Fab
  • Major prion protein
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Fab / Antibody / Octapeptide repeat / Mouse prion protein
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / response to copper ion / nucleobase-containing compound metabolic process / negative regulation of interleukin-2 production / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / negative regulation of amyloid-beta formation / cuprous ion binding / activation of protein kinase activity / negative regulation of activated T cell proliferation / negative regulation of long-term synaptic potentiation / response to amyloid-beta / negative regulation of type II interferon production / : / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / response to cadmium ion / side of membrane / inclusion body / regulation of peptidyl-tyrosine phosphorylation / cellular response to copper ion / molecular condensate scaffold activity / neuron projection maintenance / tubulin binding / protein sequestering activity / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / regulation of protein localization / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / nuclear membrane / response to oxidative stress / protease binding / mitochondrial outer membrane / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / learning or memory / copper ion binding / membrane raft / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Immunoglobulins ...Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsSwayampakula, M. / Baral, P.K. / Kav, N.N.V. / Aguzzi, A. / James, M.N.G.
CitationJournal: Protein Sci. / Year: 2013
Title: The crystal structure of an octapeptide repeat of the Prion protein in complex with a Fab fragment of the POM2 antibody.
Authors: Swayampakula, M. / Baral, P.K. / Aguzzi, A. / Kav, N.N. / James, M.N.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 26, 2014Group: Other
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Light chain of POM2 Fab
B: Heavy chain of POM2 Fab
I: Major prion protein
C: Light chain of POM2 Fab
D: Heavy chain of POM2 Fab
J: Major prion protein


Theoretical massNumber of molelcules
Total (without water)95,9126
Polymers95,9126
Non-polymers00
Water2,972165
1
A: Light chain of POM2 Fab
B: Heavy chain of POM2 Fab
I: Major prion protein


Theoretical massNumber of molelcules
Total (without water)47,9563
Polymers47,9563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-31 kcal/mol
Surface area19460 Å2
MethodPISA
2
C: Light chain of POM2 Fab
D: Heavy chain of POM2 Fab
J: Major prion protein


Theoretical massNumber of molelcules
Total (without water)47,9563
Polymers47,9563
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-31 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.415, 71.567, 207.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Antibody Light chain of POM2 Fab


Mass: 23133.510 Da / Num. of mol.: 2 / Fragment: unp residues 67-82 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Heavy chain of POM2 Fab


Mass: 23188.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Major prion protein / PrP / PrP27-30 / PrP33-35C


Mass: 1633.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P04925
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG 1000, 0.1M HEPES, 0.2M Calcium Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2011
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→39.6 Å / Num. all: 44155 / Num. obs: 44080 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.24 % / Biso Wilson estimate: 47.98 Å2 / Net I/σ(I): 10.82
Reflection shellResolution: 2.3→2.35 Å / % possible all: 98

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
autoXDSdata reduction
autoXDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DGI

4dgi


Resolution: 2.303→39.597 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 27.31 / Stereochemistry target values: ML
Details: The Rmeas for the data collection is 0.161 (overall data)
RfactorNum. reflection% reflection
Rfree0.2574 2215 5.03 %
Rwork0.2468 --
obs0.2474 44006 99.83 %
all-41792 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 2.3 Å
Refinement stepCycle: LAST / Resolution: 2.303→39.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6626 0 0 165 6791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0286797
X-RAY DIFFRACTIONf_angle_d1.9339247
X-RAY DIFFRACTIONf_dihedral_angle_d15.782403
X-RAY DIFFRACTIONf_chiral_restr0.1671040
X-RAY DIFFRACTIONf_plane_restr0.0131179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3029-2.3530.34711380.34062504X-RAY DIFFRACTION98
2.353-2.40770.32091370.34982592X-RAY DIFFRACTION100
2.4077-2.46790.39551380.34012569X-RAY DIFFRACTION100
2.4679-2.53460.34021320.32872574X-RAY DIFFRACTION100
2.5346-2.60920.34461300.31692600X-RAY DIFFRACTION100
2.6092-2.69340.30351400.31722567X-RAY DIFFRACTION100
2.6934-2.78970.32931460.31042564X-RAY DIFFRACTION100
2.7897-2.90130.32041240.29822605X-RAY DIFFRACTION100
2.9013-3.03330.30671300.28082623X-RAY DIFFRACTION100
3.0333-3.19320.32081490.27432578X-RAY DIFFRACTION100
3.1932-3.39310.29911610.25672590X-RAY DIFFRACTION100
3.3931-3.6550.25481340.23832625X-RAY DIFFRACTION100
3.655-4.02240.22661500.21842625X-RAY DIFFRACTION100
4.0224-4.60370.16861310.19122650X-RAY DIFFRACTION100
4.6037-5.79730.19841380.22684X-RAY DIFFRACTION100
5.7973-39.60310.23581370.23262841X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.0193 Å / Origin y: -13.508 Å / Origin z: 27.3858 Å
111213212223313233
T0.3912 Å2-0.0266 Å2-0.037 Å2-0.3517 Å20.0073 Å2--0.4468 Å2
L-0.1498 °2-0.1973 °20.0299 °2-0.3556 °2-0.1949 °2--0.0682 °2
S-0.0202 Å °0.0084 Å °-0.0082 Å °-0.0262 Å °0.021 Å °0.0284 Å °-0.0098 Å °-0.0005 Å °-0.0011 Å °
Refinement TLS groupSelection details: all

+
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