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

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Basic information

Entry
Database: PDB / ID: 5hoy
TitleX-ray crystallographic structure of an A-beta 17_36 beta-hairpin. X-ray diffractometer 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 / microglial cell activation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / 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 / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsKreutzer, A.G. / Spencer, R.K. / Nowick, J.S.
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
Water52229
1
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_554-y,-x,-z-1/61
Buried area13770 Å2
ΔGint-104 kcal/mol
Surface area12740 Å2
MethodPISA
2
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 area1480 Å2
ΔGint-12 kcal/mol
Surface area4730 Å2
MethodPISA
3
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_555x-y,-y,-z1
Buried area3870 Å2
ΔGint-31 kcal/mol
Surface area8550 Å2
MethodPISA
4
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 area2080 Å2
ΔGint-20 kcal/mol
Surface area4960 Å2
MethodPISA
5
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_545x,x-y-1,-z+1/61
Buried area5870 Å2
ΔGint-50 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.649, 97.649, 97.781
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-101-

HOH

21B-104-

HOH

31E-104-

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.: 29 / 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: 4.75 Å3/Da / Density % sol: 74.1 % / Description: Hexagonal pyramid
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 0.1 M HEPES Buffer, 27% (v/v) Jeffamine M-600 / PH range: 6.8-7.1 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 14, 2015
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.295→28.19 Å / Num. obs: 12832 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03762 / Net I/σ(I): 11.44
Reflection shellResolution: 2.295→2.377 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6526 / Mean I/σ(I) obs: 1.01 / % 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: 2.295→28.189 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 1284 10.01 %Random selection
Rwork0.2446 ---
obs0.2479 12832 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.295→28.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 41 29 1000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031001
X-RAY DIFFRACTIONf_angle_d0.7711333
X-RAY DIFFRACTIONf_dihedral_angle_d18.259628
X-RAY DIFFRACTIONf_chiral_restr0.044160
X-RAY DIFFRACTIONf_plane_restr0.004165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2951-2.38690.42011390.3911256X-RAY DIFFRACTION100
2.3869-2.49550.3931380.38211240X-RAY DIFFRACTION100
2.4955-2.6270.41451400.35011253X-RAY DIFFRACTION100
2.627-2.79140.39631410.34081275X-RAY DIFFRACTION100
2.7914-3.00670.32571400.30081259X-RAY DIFFRACTION100
3.0067-3.30890.261410.24821270X-RAY DIFFRACTION100
3.3089-3.78670.28691430.24871284X-RAY DIFFRACTION100
3.7867-4.76710.20311460.17931313X-RAY DIFFRACTION100
4.7671-28.19110.26221560.22391398X-RAY DIFFRACTION100
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)
11.32961.2005-2.10759.239-0.99864.0593-0.1905-0.0742-0.1121.23880.0044-0.471-1.2223-0.5487-0.14480.8329-0.01890.050.5733-0.04070.523536.9284-7.99135.7575
21.68120.38961.89278.3955-3.54643.88490.13850.1736-0.28430.0086-0.4959-0.3446-1.11310.55840.20.5585-0.0367-0.00460.5013-0.05170.474441.4144-7.6201-2.1458
35.68292.7469-2.94257.27963.59156.5052-1.78760.52141.56630.13850.69910.6207-2.3412-1.58370.93680.87120.1712-0.01050.83890.05770.588822.7508-6.1295-5.0627
47.2283-3.9827.30014.7868-2.74347.7821-0.967-0.75510.46860.81670.71790.3536-1.2283-1.49660.15920.60290.10840.13750.54160.02140.653827.6586-10.14321.4489
54.64140.1842.04445.39821.74475.3548-0.37490.30620.5572-1.06310.3817-0.8068-0.0090.7459-0.06050.75750.0810.07540.5307-0.02730.508938.7866-2.472-10.1767
63.91894.0938-3.39135.3262-2.59423.6862-0.17810.25130.2745-0.4626-0.04010.33180.004-0.13750.12310.78540.0556-0.0380.52890.02820.537730.8416-5.6209-11.9
74.95964.67622.25635.38723.74814.28471.2341-1.1222-0.44581.67780.075-0.40081.0394-0.9059-1.37430.56680.0203-0.12240.5419-0.04040.431837.7264-24.7596.7168
83.3683-2.17695.70131.4328-3.89492.0027-0.52250.8477-0.1911.23092.1056-3.2519-3.7622-1.54621.01561.5764-0.0881-0.04430.8639-0.28231.863342.3118-15.38714.3485
98.98665.83675.10195.09555.2065.85660.5539-1.3194-0.451-0.0411-0.8997-0.28760.3654-2.22260.39390.53260.046-0.04170.76990.00810.624632.3181-25.73525.7898
106.0584-2.96554.02468.69093.00116.08560.3908-1.7483-1.0765-0.2115-0.47861.05581.8901-1.72620.16470.7853-0.2336-0.23680.62410.1520.679332.3091-36.03032.6225
112.01853.6188-6.76897.2142-6.23136.9674-0.84530.6438-1.8627-1.6057-0.4354-0.35872.52640.3680.79490.79110.07180.0630.660.09540.555640.972-33.4997-4.4591
127.26312.15141.55867.0135-2.90955.9496-0.78150.5265-1.2587-0.49020.568-1.23642.10761.28070.16180.84820.25380.01030.7407-0.0020.865849.2649-30.8665-1.6518
135.7382-3.4073-2.81212.8533-0.49468.6293-0.37040.49061.15380.19920.578-1.2895-0.37430.61-0.18090.4353-0.0763-0.06490.51630.04030.679946.7059-23.0771.8507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:11 )A1 - 11
2X-RAY DIFFRACTION2( CHAIN A AND RESID 12:21 )A12 - 21
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:11 )B1 - 11
4X-RAY DIFFRACTION4( CHAIN B AND RESID 12:21 )B12 - 21
5X-RAY DIFFRACTION5( CHAIN C AND RESID 1:11 )C1 - 11
6X-RAY DIFFRACTION6( CHAIN C AND RESID 12:21 )C12 - 21
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:6 )D1 - 6
8X-RAY DIFFRACTION8( CHAIN D AND RESID 7:12 )D7 - 12
9X-RAY DIFFRACTION9( CHAIN D AND RESID 13:21 )D13 - 21
10X-RAY DIFFRACTION10( CHAIN E AND RESID 1:13 )E1 - 13
11X-RAY DIFFRACTION11( CHAIN E AND RESID 14:21 )E14 - 21
12X-RAY DIFFRACTION12( CHAIN F AND RESID 1:11 )F1 - 11
13X-RAY DIFFRACTION13( CHAIN F AND RESID 12:21 )F12 - 21

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