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- PDB-3ovj: Structure of an amyloid forming peptide KLVFFA from amyloid beta ... -

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Basic information

Entry
Database: PDB / ID: 3ovj
TitleStructure of an amyloid forming peptide KLVFFA from amyloid beta in complex with orange G
ComponentsKLVFFA hexapeptide segment from Amyloid beta
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Function / homology
Function and homology information


regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / ionotropic glutamate receptor signaling pathway / positive regulation of protein metabolic process / neuron projection maintenance / cholesterol metabolic process / extracellular matrix organization / positive regulation of glycolytic process / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / learning / central nervous system development / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / synapse organization / Post-translational protein phosphorylation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / Golgi lumen / neuron cellular homeostasis / endocytosis / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation
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. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 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
Chem-ORA / Amyloid-beta precursor protein
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLandau, M. / Eisenberg, D.
CitationJournal: Plos Biol. / Year: 2011
Title: Towards a pharmacophore for amyloid.
Authors: Landau, M. / Sawaya, M.R. / Faull, K.F. / Laganowsky, A. / Jiang, L. / Sievers, S.A. / Liu, J. / Barrio, J.R. / Eisenberg, D.
History
DepositionSep 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: KLVFFA hexapeptide segment from Amyloid beta
B: KLVFFA hexapeptide segment from Amyloid beta
C: KLVFFA hexapeptide segment from Amyloid beta
D: KLVFFA hexapeptide segment from Amyloid beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7166
Polymers2,9004
Non-polymers8172
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)9.536, 26.008, 25.803
Angle α, β, γ (deg.)62.280, 88.590, 88.450
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a pair of beta sheets with orange G interrelating between the sheets. The fiber is constructed from unit cell translations along the a direction (i.e. X+1,Y,Z; X+2,Y,Z; X+3,Y,Z, etc.).

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Components

#1: Protein/peptide
KLVFFA hexapeptide segment from Amyloid beta


Mass: 724.909 Da / Num. of mol.: 4 / Fragment: KLVFFA (UNP residues 687-692) / Source method: obtained synthetically
Details: KLVFFA (residues 16-21) from Amyloid beta, synthesized
References: UniProt: P05067
#2: Chemical ChemComp-ORA / 7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid / Orange G / Orange G


Mass: 408.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12N2O7S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.9537.01
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2911vapor diffusion, hanging dropreservoir contained 30% w/v Polyethylene glycol 1,500, 20% v/v Glycerol, vapor diffusion, hanging drop, temperature 291K
2912vapor diffusion, hanging dropreservoir contained 10% w/v Polyethylene glycol 1,500, 30% v/v Glycerol, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.9792
SYNCHROTRONAPS 24-ID-E20.9792
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 16, 2008
ADSC QUANTUM 3152CCDNov 13, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. all: 1870 / Num. obs: 1870 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.189 / Χ2: 1.054 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.941.70.4143041.031,271.7
1.94-2.132.10.3653671.0341,292.7
2.13-2.444.10.3874021.0481,296.2
2.44-3.0850.3074031.0691,299.8
3.08-905.40.1633941.0531,298

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å23.04 Å
Translation1.9 Å23.04 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2335 / WRfactor Rwork: 0.2255 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.824 / SU B: 4.528 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2654 / SU Rfree: 0.1689 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 172 9.2 %RANDOM
Rwork0.2054 ---
all0.2067 1864 --
obs0.2067 1864 91.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 39.53 Å2 / Biso mean: 16.4603 Å2 / Biso min: 4.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.07 Å20.03 Å2
2---0.1 Å2-0.11 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms208 0 54 11 273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023270
X-RAY DIFFRACTIONr_bond_other_d0.0050.02166
X-RAY DIFFRACTIONr_angle_refined_deg1.692.229368
X-RAY DIFFRACTIONr_angle_other_deg0.693392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.107520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8621536
X-RAY DIFFRACTIONr_chiral_restr0.0910.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0278
X-RAY DIFFRACTIONr_mcbond_it1.2141.5120
X-RAY DIFFRACTIONr_mcbond_other0.261.544
X-RAY DIFFRACTIONr_mcangle_it2.112188
X-RAY DIFFRACTIONr_scbond_it3.1913150
X-RAY DIFFRACTIONr_scangle_it5.0974.5180
LS refinement shellResolution: 1.803→2.015 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.366 26 -
Rwork0.289 434 -
all-460 -
obs--79.86 %

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