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- PDB-3q2x: Structure of an amyloid forming peptide NKGAII (residues 27-32) f... -

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Basic information

Entry
Database: PDB / ID: 3q2x
TitleStructure of an amyloid forming peptide NKGAII (residues 27-32) from amyloid beta
ComponentsAmyloid beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid protofibril
Function / homology
Function and homology information


cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / NMDA selective glutamate receptor signaling pathway / microglia development / regulation of Wnt signaling pathway / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity ...cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / NMDA selective glutamate receptor signaling pathway / microglia development / regulation of Wnt signaling pathway / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Golgi-associated vesicle / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / COPII-coated ER to Golgi transport vesicle / suckling behavior / nuclear envelope lumen / dendrite development / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / regulation of presynapse assembly / transition metal ion binding / regulation of multicellular organism growth / negative regulation of neuron differentiation / intracellular copper ion homeostasis / ECM proteoglycans / positive regulation of T cell migration / spindle midzone / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / protein serine/threonine kinase binding / regulation of peptidyl-tyrosine phosphorylation / clathrin-coated pit / positive regulation of chemokine production / forebrain development / Notch signaling pathway / neuron projection maintenance / Mitochondrial protein degradation / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / cholesterol metabolic process / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / response to interleukin-1 / extracellular matrix organization / positive regulation of mitotic cell cycle / axonogenesis / adult locomotory behavior / platelet alpha granule lumen / trans-Golgi network membrane / learning / positive regulation of interleukin-1 beta production / dendritic shaft / positive regulation of peptidyl-threonine phosphorylation / positive regulation of long-term synaptic potentiation / central nervous system development / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / serine-type endopeptidase inhibitor activity / neuromuscular junction / visual learning / recycling endosome / cognition / Golgi lumen / positive regulation of inflammatory response / positive regulation of interleukin-6 production / neuron cellular homeostasis / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction / synaptic vesicle / Platelet degranulation / apical part of cell
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. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...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. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.451 Å
AuthorsSoriaga, A.B. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Molecular basis for amyloid-beta polymorphism.
Authors: Colletier, J.P. / Laganowsky, A. / Landau, M. / Zhao, M. / Soriaga, A.B. / Goldschmidt, L. / Flot, D. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Sep 13, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)6161
Polymers6161
Non-polymers00
Water362
1
A: Amyloid beta A4 protein
x 6


Theoretical massNumber of molelcules
Total (without water)3,6946
Polymers3,6946
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_565-x,y+3/2,-z1
crystal symmetry operation2_575-x,y+5/2,-z1
Unit cell
Length a, b, c (Å)15.074, 4.838, 24.016
Angle α, β, γ (deg.)90.000, 95.560, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a pair of beta sheets with the side chains interdigitating between the sheets. One sheet is constructed from unit cell translations along the b direction (i.e. X,Y+1,Z; X,Y+2,Z; X,Y+3,Z, etc.). The other sheet is constructed from symmetry operators -X+1,Y+1/2,-Z+1; -X+1,Y+3/2,-Z+1; -X+1,Y+5/2,-Z+1, etc.

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Components

#1: Protein/peptide Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid precursor protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 615.743 Da / Num. of mol.: 1 / Fragment: NKGAII hexapeptide segment (UNP residues 698-703) / Source method: obtained synthetically
Details: NKGAII (residues 27-32) from human Amyloid beta, synthesized
Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.42 Å3/Da / Density % sol: 13.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: reservoir contained 2.4M Sodium Malonate, 15% v/v Glycerol, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. all: 671 / Num. obs: 671 / % possible obs: 90.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.122 / Χ2: 1.07 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.53.20.322701.129194.6
1.5-1.562.90.224611.003184.7
1.56-1.633.10.169551.091175.3
1.63-1.7230.169631.006198.4
1.72-1.8330.135631.033196.9
1.83-1.973.50.152681.099191.9
1.97-2.173.70.137751.063198.7
2.17-2.483.20.108731.07190.1
2.48-3.1230.127661.11194.3
3.12-1002.90.063771.073186.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.451→23.903 Å / Occupancy max: 1 / Occupancy min: 0.89 / FOM work R set: 0.8252 / SU ML: 0.18 / σ(F): 0.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 71 10.82 %RANDOM
Rwork0.2041 ---
obs0.2095 656 88.77 %-
all-656 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.001 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso max: 13.08 Å2 / Biso mean: 4.9282 Å2 / Biso min: 0.63 Å2
Baniso -1Baniso -2Baniso -3
1--3.441 Å2-0 Å2-0.7136 Å2
2---3.622 Å20 Å2
3---2.0179 Å2
Refinement stepCycle: LAST / Resolution: 1.451→23.903 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms43 0 0 2 45
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01142
X-RAY DIFFRACTIONf_angle_d1.86955
X-RAY DIFFRACTIONf_chiral_restr0.0937
X-RAY DIFFRACTIONf_plane_restr0.0057
X-RAY DIFFRACTIONf_dihedral_angle_d7.4516
LS refinement shellHighest resolution: 1.4506 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2589 71 -
Rwork0.2041 585 -
all-656 -
obs--89 %

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