[English] 日本語
Yorodumi
- PDB-1nmj: The Solution Structure of Rat Ab-(1-28) and its Interaction with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nmj
TitleThe Solution Structure of Rat Ab-(1-28) and its Interaction with Zinc: Insights into the Scarity of Amyloid Deposition in Aged Rat Brain
Componentsamyloid beta-peptide from Alzheimer's disease amyloid A4 protein homolog
KeywordsMEMBRANE PROTEIN / Glycoprotein / Amyloid
Function / homology
Function and homology information


Formyl peptide receptors bind formyl peptides and many other ligands / ECM proteoglycans / TAK1-dependent IKK and NF-kappa-B activation / Post-translational protein phosphorylation / TRAF6 mediated NF-kB activation / endosome to plasma membrane transport vesicle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Advanced glycosylation endproduct receptor signaling / negative regulation of presynapse assembly / Mitochondrial protein degradation ...Formyl peptide receptors bind formyl peptides and many other ligands / ECM proteoglycans / TAK1-dependent IKK and NF-kappa-B activation / Post-translational protein phosphorylation / TRAF6 mediated NF-kB activation / endosome to plasma membrane transport vesicle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Advanced glycosylation endproduct receptor signaling / negative regulation of presynapse assembly / Mitochondrial protein degradation / Platelet degranulation / cytosolic mRNA polyadenylation / synaptic assembly at neuromuscular junction / Lysosome Vesicle Biogenesis / smooth endoplasmic reticulum calcium ion homeostasis / lipoprotein particle / regulation of amyloid-beta clearance / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / ciliary rootlet / suckling behavior / COPII-coated ER to Golgi transport vesicle / frizzled binding / amyloid-beta complex / heparan sulfate proteoglycan binding / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / regulation of synapse structure or activity / axo-dendritic transport / axon midline choice point recognition / astrocyte activation involved in immune response / G alpha (q) signalling events / presynaptic active zone / regulation of spontaneous synaptic transmission / G alpha (i) signalling events / mating behavior / growth factor receptor binding / peptidase activator activity / neuromuscular process controlling balance / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / astrocyte projection / neuron remodeling / negative regulation of neuron differentiation / nuclear envelope lumen / spindle midzone / intracellular vesicle / forebrain development / positive regulation of protein metabolic process / dendrite development / smooth endoplasmic reticulum / modulation of excitatory postsynaptic potential / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / apolipoprotein binding / main axon / transition metal ion binding / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T cell migration / neuronal dense core vesicle / cholesterol metabolic process / positive regulation of chemokine production / cellular response to manganese ion / clathrin-coated pit / Notch signaling pathway / extracellular matrix organization / neuron projection maintenance / astrocyte activation / ionotropic glutamate receptor signaling pathway / axonogenesis / response to interleukin-1 / positive regulation of mitotic cell cycle / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / cellular response to copper ion / cellular response to cAMP / positive regulation of glycolytic process / adult locomotory behavior / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / dendritic shaft / learning / positive regulation of JNK cascade / locomotory behavior / neuromuscular junction / microglial cell activation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / cellular response to nerve growth factor stimulus / neuron cellular homeostasis / visual learning
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR
AuthorsHuang, J. / Yao, Y. / Tang, W.X.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2004
Title: The solution structure of rat Abeta-(1-28) and its interaction with zinc ion: insights into the scarcity of amyloid deposition in aged rat brain
Authors: Huang, J. / Yao, Y. / Lin, J. / Ye, Y.H. / Sun, W.Y. / Tang, W.X.
History
DepositionJan 10, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: amyloid beta-peptide from Alzheimer's disease amyloid A4 protein homolog


Theoretical massNumber of molelcules
Total (without water)3,1711
Polymers3,1711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein/peptide amyloid beta-peptide from Alzheimer's disease amyloid A4 protein homolog


Mass: 3171.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P08592

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D TOCSY
131DQF-COSY

-
Sample preparation

DetailsContents: 2mM rat ab-(1-28) / Solvent system: DMSO
Sample conditionsTemperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

-
Processing

NMR ensembleConformers submitted total number: 1

+
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