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- PDB-4pqd: The longer crystal structure of the grow factor like domain from ... -

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Basic information

Entry
Database: PDB / ID: 4pqd
TitleThe longer crystal structure of the grow factor like domain from Beta amypoid precusor protein (APP22-126)
ComponentsAmyloid beta A4 protein
KeywordsPROTEIN BINDING / Alphan and Beta / Growth factor / Heparin binding / Alzheimer's Disease / Death receptor 6 binding
Function / homology
Function and homology information


amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / positive regulation of protein metabolic process / neuromuscular process controlling balance / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / regulation of presynapse assembly / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / 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 / platelet alpha granule lumen / adult locomotory behavior / positive regulation of glycolytic process / central nervous system development / learning / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / visual learning / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / neuron projection development / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / apical part of cell / synaptic vesicle / cell-cell junction / Platelet degranulation
Similarity search - Function
Sugar Binding Protein, Amyloid A4 Protein; Chain A / Amyloidogenic glycoprotein, heparin-binding domain / 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 ...Sugar Binding Protein, Amyloid A4 Protein; Chain A / Amyloidogenic glycoprotein, heparin-binding domain / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.332 Å
AuthorsTan, X. / Li, W. / Wang, Z.
CitationJournal: To be Published
Title: Mapping the interaction betwwen APP and DR6
Authors: Tan, X. / Li, W. / Wang, Z.
History
DepositionMar 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)11,8401
Polymers11,8401
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.755, 49.025, 65.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II / N-APP / Soluble APP-alpha / S-APP-alpha / Soluble APP-beta / S-APP-beta / C99 / Beta-amyloid protein 42 / Beta-APP42 / Beta-amyloid protein 40 / Beta-APP40 / C83 / P3(42) / P3(40) / C80 / Gamma-secretase C-terminal fragment 59 / Amyloid intracellular domain 59 / AICD-59 / AID(59) / Gamma-CTF(59) / Gamma-secretase C-terminal fragment 57 / Amyloid intracellular domain 57 / AICD-57 / AID(57) / Gamma-CTF(57) / Gamma-secretase C-terminal fragment 50 / Amyloid intracellular domain 50 / AICD-50 / AID(50) / Gamma-CTF(50) / C31


Mass: 11840.482 Da / Num. of mol.: 1
Fragment: the N-terminal GFLD doamin of APP, UNP residues 22-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05067
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% v/v TacsimateTM pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.33→27.23 Å / Num. all: 23021 / Num. obs: 22664 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.33-1.36154
1.36-1.4168
1.4-1.44180
1.44-1.48191
1.48-1.54199
1.54-1.61100
1.6-1.671100
1.67-1.761100
1.76-1.871100
1.87-2.021100
2.02-2.221100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.332→27.23 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 1998 8.82 %random
Rwork0.1696 ---
obs0.171 22664 91.72 %-
all-23021 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.332→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 0 161 986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007846
X-RAY DIFFRACTIONf_angle_d1.1041143
X-RAY DIFFRACTIONf_dihedral_angle_d12.32314
X-RAY DIFFRACTIONf_chiral_restr0.081124
X-RAY DIFFRACTIONf_plane_restr0.005151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3317-1.3650.1843830.1929862X-RAY DIFFRACTION54
1.365-1.40190.20251040.17161065X-RAY DIFFRACTION68
1.4019-1.44310.16371210.17721252X-RAY DIFFRACTION80
1.4431-1.48970.18971420.17731467X-RAY DIFFRACTION91
1.4897-1.54290.18691490.16941554X-RAY DIFFRACTION99
1.5429-1.60470.18171510.16351576X-RAY DIFFRACTION100
1.6047-1.67770.19321550.16921594X-RAY DIFFRACTION100
1.6777-1.76610.17721530.16581583X-RAY DIFFRACTION100
1.7661-1.87680.18621560.16611604X-RAY DIFFRACTION100
1.8768-2.02160.20191550.15721600X-RAY DIFFRACTION100
2.0216-2.2250.15631560.15321621X-RAY DIFFRACTION100
2.225-2.54680.1781590.16551636X-RAY DIFFRACTION100
2.5468-3.20790.19431580.1741634X-RAY DIFFRACTION100
3.2079-27.24110.19751560.18041618X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2684.37511.45025.0709-0.71388.7089-0.02370.6671-0.7492-0.40460.0363-0.79390.96340.67740.01140.25310.03440.04440.2892-0.06950.296246.71275.21759.7527
22.8233-1.7118-1.58664.1141.66492.55680.0252-0.11380.2588-0.05730.0279-0.0339-0.085-0.0956-0.03470.0682-0.01450.00660.05130.01610.063225.179117.902316.5433
35.3592-2.3943-0.63394.50210.15023.64990.11490.5535-0.1782-0.338-0.1615-0.01390.10380.03810.05050.080.0070.00990.1306-0.030.079329.054912.806710.6486
42.16660.9372.72862.20521.45446.3676-0.0073-0.1229-0.0160.0762-0.03940.3069-0.0387-0.54860.04530.0822-0.00850.01080.1285-0.00450.115817.30115.061820.1457
52.7671-2.5866-1.67735.71612.11267.0719-0.0398-0.0911-0.16260.22670.00370.12530.07960.02150.07610.061-0.00860.01430.08160.0040.089123.791711.668525.5774
60.9524-0.36350.27753.2681-1.43652.1994-0.0389-0.00380.00310.1554-0.0588-0.1791-0.05730.1610.09050.0566-0.00060.00410.0772-0.00610.076731.631814.967921.4978
74.26094.1902-1.08945.1311-0.66241.4274-0.55850.9280.286-0.99520.53850.6237-0.0974-0.1978-0.0240.2579-0.0457-0.06030.23280.03820.206817.562920.10847.4759
81.2881-1.24741.06482.8094-2.22313.26610.05460.0201-0.04120.1516-0.06730.03350.13170.1550.03710.0753-0.0009-0.00490.0561-0.0050.057932.974813.271825.9261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 65 )
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 76 )
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 94 )
7X-RAY DIFFRACTION7chain 'A' and (resid 95 through 109 )
8X-RAY DIFFRACTION8chain 'A' and (resid 110 through 126 )

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