[English] 日本語
Yorodumi
- PDB-2li9: Metal binding domain of rat beta-amyloid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2li9
TitleMetal binding domain of rat beta-amyloid
ComponentsAmyloid beta A4 protein
KeywordsCELL ADHESION / Alzheimer's disease / Dimer formation / Zinc binding
Function / homology
Function and homology information


Formyl peptide receptors bind formyl peptides and many other ligands / growth cone lamellipodium / cellular response to norepinephrine stimulus / ECM proteoglycans / growth cone filopodium / 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) ...Formyl peptide receptors bind formyl peptides and many other ligands / growth cone lamellipodium / cellular response to norepinephrine stimulus / ECM proteoglycans / growth cone filopodium / 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 / Mitochondrial protein degradation / Platelet degranulation / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / lipoprotein particle / regulation of amyloid-beta clearance / peptidase activator activity / growth factor receptor binding / astrocyte projection / frizzled binding / amyloid-beta complex / heparan sulfate proteoglycan binding / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / synaptic assembly at neuromuscular junction / axo-dendritic transport / G alpha (q) signalling events / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / G alpha (i) signalling events / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / main axon / PTB domain binding / positive regulation of amyloid fibril formation / neuron remodeling / nuclear envelope lumen / intracellular vesicle / COPII-coated ER to Golgi transport vesicle / suckling behavior / neuronal dense core vesicle / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / presynaptic active zone / positive regulation of protein metabolic process / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / apolipoprotein binding / regulation of presynapse assembly / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / cellular response to manganese ion / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / forebrain development / positive regulation of chemokine production / clathrin-coated pit / cellular response to copper ion / Notch signaling pathway / cellular response to cAMP / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / response to interleukin-1 / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / axonogenesis / positive regulation of calcium-mediated signaling / dendritic shaft / adult locomotory behavior / positive regulation of glycolytic process / central nervous system development / learning / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / astrocyte activation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / cellular response to nerve growth factor stimulus / response to lead ion / synapse organization / positive regulation of non-canonical NF-kappaB signal transduction / terminal bouton / neuromuscular junction
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 / simulated annealing, QM, MM geometry optimization
Model detailsclosest to the average, model 1
AuthorsPolshakov, V. / Istrate, A. / Kozin, S. / Makarov, A.
Citation
Journal: Biophys.J. / Year: 2012
Title: NMR solution structure of rat Abeta(1-16): toward understanding the mechanism of rats' resistance to Alzheimer's disease.
Authors: Istrate, A.N. / Tsvetkov, P.O. / Mantsyzov, A.B. / Kulikova, A.A. / Kozin, S.A. / Makarov, A.A. / Polshakov, V.I.
#1: Journal: MOL.BIOL.(MOSCOW) / Year: 2010
Title: Optimization of the methods for small peptide solution structure determination by NMR spectroscopy.
Authors: Istrate, A.N. / Mantsyzov, A.B. / Kozin, S.A. / Pol'shakov, V.I.
History
DepositionAug 25, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8393
Polymers3,7742
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide Amyloid beta A4 protein / ABPP / APP / Alzheimer disease amyloid A4 protein homolog / Amyloidogenic glycoprotein / AG


Mass: 1886.998 Da / Num. of mol.: 2 / Fragment: UNP residues 672-687 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P08592
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR solution structure of the dimer of rat beta-Amyloid metal binding domain complexed with zinc ion
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-13C HSQC
1212D DQF-COSY
1322D DQF-COSY
1412D 1H-1H NOESY
1522D 1H-1H NOESY
1622D 1H-1H TOCSY
1712D 1H-1H TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
15 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
25 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMentity_1-11
8 mMZinc cloride-21
20 mMTRIS-3[U-100% 2H]1
0.1 %sodium azide-41
5 mMentity_1-52
8 mMZinc cloride-62
20 mMTRIS-7[U-100% 2H]2
0.1 %sodium azide-82
Sample conditionsIonic strength: 10 / pH: 7.1 / Pressure: ambient / Temperature: 278 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
AnglesearchV. Polshakovdata analysis
GROMACS3.3.1Van Der Spoel et al.structure solution
GROMACS/CPMDBiswas & Gogoneageometry optimization
ProcheckNMRLaskowski and MacArthurdata analysis
Insight IIAccelrys Software Inc.data analysis
GROMACSVan Der Spoel et al.refinement
GROMACS/CPMDBiswas & Gogonearefinement
RefinementMethod: simulated annealing, QM, MM geometry optimization / Software ordinal: 1 / Details: simulation in explicit water environment
NMR constraintsNOE intraresidue total count: 144 / NOE medium range total count: 30 / NOE sequential total count: 66
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

+
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