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- PDB-2li9: Metal binding domain of rat beta-amyloid -

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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 / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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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

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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

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NMR measurement

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

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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

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