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- PDB-5hox: X-ray crystallographic structure of an A-beta 17_36 beta-hairpin.... -

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Basic information

Entry
Database: PDB / ID: 5hox
TitleX-ray crystallographic structure of an A-beta 17_36 beta-hairpin. Synchrotron data set. (LVFFAEDCGSNKCAII(SAR)LMV).
ComponentsAmyloid beta A4 protein
KeywordsDE NOVO PROTEIN / amyloid / oligomer / beta-hairpin / Alzheimer's / PROTEIN FIBRIL
Function / homology
Function and homology information


regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / 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 / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / 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 / positive regulation of amyloid fibril formation / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / 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 / negative regulation of long-term synaptic potentiation / 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 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 / cholesterol metabolic process / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / neuron projection maintenance / positive regulation of glycolytic process / extracellular matrix organization / 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 / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / Post-translational protein phosphorylation / synapse organization / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / neuromuscular junction / visual learning / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / positive regulation of interleukin-6 production / neuron cellular homeostasis / Golgi lumen / endocytosis / 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) / neuron projection development / cellular response to amyloid-beta / 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-JEF / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKreutzer, A.G. / Nowick, J.S. / Spencer, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: X-ray Crystallographic Structures of a Trimer, Dodecamer, and Annular Pore Formed by an A beta 17-36 beta-Hairpin.
Authors: Kreutzer, A.G. / Hamza, I.L. / Spencer, R.K. / Nowick, J.S.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1567
Polymers13,5586
Non-polymers5981
Water68538
1
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)6,7793
Polymers6,7793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area4740 Å2
MethodPISA
2
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein

A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)13,5586
Polymers13,5586
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_677x-y+1,-y+2,-z+21
Buried area3870 Å2
ΔGint-29 kcal/mol
Surface area8580 Å2
MethodPISA
3
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3774
Polymers6,7793
Non-polymers5981
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-20 kcal/mol
Surface area4950 Å2
MethodPISA
4
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
hetero molecules

D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7548
Polymers13,5586
Non-polymers1,1962
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_577x,x-y+2,-z+13/61
Buried area5900 Å2
ΔGint-53 kcal/mol
Surface area8190 Å2
MethodPISA
5
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
hetero molecules

A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,31214
Polymers27,11712
Non-polymers1,1962
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_776-y+2,-x+2,-z+11/61
Buried area13740 Å2
ΔGint-100 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.369, 97.369, 97.591
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-104-

HOH

21F-201-

HOH

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Components

#1: Protein/peptide
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


Mass: 2259.730 Da / Num. of mol.: 6 / Fragment: UNP residues 687-707 / Mutation: V24C, G29C, G33Sar / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#2: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 4.71 Å3/Da / Density % sol: 73.9 % / Description: Hexagonal pyramid
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 0.1 M HEPES Buffer, 29% (v/v) Jeffamine M-600 / PH range: 6.5 - 7.5 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 1.9→30.35 Å / Num. obs: 22069 / % possible obs: 99 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.01344 / Net I/σ(I): 13.82
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 2 % / Rmerge(I) obs: 0.9116 / Mean I/σ(I) obs: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLM7.2.1data reduction
Aimless0.5.17data scaling
PHASER1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HOW

5how


Resolution: 1.9→30.35 Å / Cross valid method: FREE R-VALUE / Phase error: 29.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1987 9.06 %Random selection
Rwork0.2199 ---
obs0.2227 21935 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→30.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 41 38 1009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019998
X-RAY DIFFRACTIONf_angle_d1.6231327
X-RAY DIFFRACTIONf_dihedral_angle_d20.068619
X-RAY DIFFRACTIONf_chiral_restr0.082160
X-RAY DIFFRACTIONf_plane_restr0.011165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94760.42991280.41811301X-RAY DIFFRACTION92
1.9476-2.00020.40281390.35341390X-RAY DIFFRACTION100
2.0002-2.05910.31781410.32241413X-RAY DIFFRACTION100
2.0591-2.12560.32521390.3031401X-RAY DIFFRACTION100
2.1256-2.20150.27231400.27071395X-RAY DIFFRACTION100
2.2015-2.28970.34271400.28681407X-RAY DIFFRACTION100
2.2897-2.39390.28651420.25071422X-RAY DIFFRACTION100
2.3939-2.52010.35111400.26551407X-RAY DIFFRACTION100
2.5201-2.6780.2931420.26891435X-RAY DIFFRACTION100
2.678-2.88480.2771440.2341437X-RAY DIFFRACTION100
2.8848-3.17510.25961430.22051435X-RAY DIFFRACTION100
3.1751-3.63450.24291470.19851466X-RAY DIFFRACTION100
3.6345-4.57890.19581460.17371473X-RAY DIFFRACTION100
4.5789-63.84120.23631560.21411566X-RAY DIFFRACTION98
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)
15.91450.15553.69347.6235-1.9015.8855-0.0251-0.73330.19462.2187-0.02380.08490.5691-0.2246-0.08421.1598-0.0455-0.01620.5250.050.514211.838992.3364103.3953
21.8894-2.93922.28365.2269-4.87754.94910.2454-0.13150.1111-0.2593-0.1572-0.1081.2858-0.8334-0.08930.7017-0.042-0.01070.46590.05140.42477.465391.93295.5158
34.42814.5712-2.15197.526-2.3365.4722-2.16080.4765-2.00180.26840.4993-1.30021.7151.3761.65790.80730.180.10510.89890.09540.691726.355190.474892.6826
46.3731-1.7839-5.91155.75292.33925.656-0.5842-0.90330.82820.68160.7952-1.02690.40671.8073-0.14860.66610.1106-0.09670.6116-0.00340.548921.160494.395799.0204
53.2053-0.039-3.97528.8323-1.88825.40540.37190.2935-0.5824-0.933-0.03661.38281.2897-0.8198-0.60980.9937-0.0046-0.19190.5320.04670.55759.946786.738987.4
63.24780.26361.75155.69181.95963.4078-0.94120.4319-0.7033-1.19550.5067-0.63860.49630.50450.57050.72460.0845-0.01660.4067-0.00360.430517.915789.864685.7527
76.09554.74251.3456.5054-2.34935.19560.7311-1.69110.18460.9886-0.48770.1408-0.01040.9237-0.48380.5430.01830.12380.5415-0.01850.432411.1126108.9691104.2795
85.4178-5.48223.82939.9329-1.19074.2879-1.4902-0.3088-0.7071.27773.25014.1891.9824.938-2.01971.28840.29010.12431.82830.37781.34426.21699.2071111.6806
94.07995.025-4.77337.6609-6.42435.7588-0.0758-1.4432-0.212-0.1644-0.6066-0.3280.33262.09440.71370.58770.01030.08140.78640.03440.437816.4769109.9173103.347
105.88356.35083.21837.75525.2594.6126-0.5195-1.06570.8925-0.88650.2670.1395-3.2141-0.2180.65440.603-0.0810.09660.45-0.09190.46089.7841116.364198.4677
113.1487-4.0808-0.85035.44531.48031.54010.616-2.10131.5740.8064-1.1589-3.0221-1.18472.14730.52331.0408-0.34850.23061.3684-0.18571.121221.7651123.085101.5824
125.27635.27593.69126.09455.26245.0345-0.9990.7480.9725-0.98810.38510.2564-2.5960.04230.50640.6917-0.0542-0.02080.6434-0.08740.52497.8635117.722593.1092
134.3178-1.16373.79194.0451-3.64385.3627-0.5948-0.0548-0.27210.4540.14351.651-0.646-1.72310.45720.54030.14070.03590.5318-0.05020.6323.2077111.429898.9031
142.0223-2.97163.49044.5206-4.53329.19823.60737.0526.4972-2.101-1.4936-0.50713.231-1.1502-1.0291.58370.1034-0.14231.94130.51461.7279-5.4391120.584892.3764
154.59140.11453.44724.109-3.13815.66090.07340.4005-2.0423-0.40940.19552.13460.7289-0.7083-0.25060.48190.01130.08530.5251-0.07360.6092.7566105.931499.8183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 21 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 11 )
4X-RAY DIFFRACTION4chain 'B' and (resid 12 through 21 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 11 )
6X-RAY DIFFRACTION6chain 'C' and (resid 12 through 21 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 6 )
8X-RAY DIFFRACTION8chain 'D' and (resid 7 through 12 )
9X-RAY DIFFRACTION9chain 'D' and (resid 13 through 21 )
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'E' and (resid 6 through 13 )
12X-RAY DIFFRACTION12chain 'E' and (resid 14 through 21 )
13X-RAY DIFFRACTION13chain 'F' and (resid 1 through 6 )
14X-RAY DIFFRACTION14chain 'F' and (resid 7 through 12 )
15X-RAY DIFFRACTION15chain 'F' and (resid 13 through 21 )

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